Isolated polynucleotides and polypeptides, and methods of using same for increasing plant yield and/or agricultural characteristics

ABSTRACT

Provided are isolated polypeptides which are at least 80% homologous to SEQ ID NOs: 710-1153 and 9276-15726, isolated polynucleotides which are at least 80% identical to SEQ ID NOs: 1-709 and 1157-9275, nucleic acid constructs comprising same, transgenic cells expressing same, transgenic plants expressing same and method of using same for increasing yield, abiotic stress tolerance, growth rate, biomass, vigor, oil content, photosynthetic capacity, seed yield, fiber yield, fiber quality, fiber length, and/or nitrogen use efficiency of a plant.

FIELD AND BACKGROUND OF THE INVENTION

The present invention, in some embodiments thereof, relates to isolatedpolypeptides and polynucleotides, nucleic acid constructs comprisingsame, transgenic cells comprising same, transgenic plants exogenouslyexpressing same and more particularly, but not exclusively, to methodsof using same for increasing yield (e.g., seed yield, oil yield),biomass, growth rate, vigor, oil content, fiber yield, fiber quality,fiber length, fiber length, photosynthetic capacity, fertilizer useefficiency (e.g., nitrogen use efficiency) and/or abiotic stresstolerance of a plant.

Yield is affected by various factors, such as, the number and size ofthe plant organs, plant architecture (for example, the number ofbranches), grains set length, number of filled grains, vigor (e.g.seedling), growth rate, root development, utilization of water,nutrients (e.g., nitrogen) and fertilizers, and stress tolerance.

Crops such as, corn, rice, wheat, canola and soybean account for overhalf of total human caloric intake, whether through direct consumptionof the seeds themselves or through consumption of meat products raisedon processed seeds or forage. Seeds are also a source of sugars,proteins and oils and metabolites used in industrial processes. Theability to increase plant yield, whether through increase dry matteraccumulation rate, modifying cellulose or lignin composition, increasestalk strength, enlarge meristem size, change of plant branchingpattern, erectness of leaves, increase in fertilization efficiency,enhanced seed dry matter accumulation rate, modification of seeddevelopment, enhanced seed filling or by increasing the content of oil,starch or protein in the seeds would have many applications inagricultural and non-agricultural uses such as in the biotechnologicalproduction of pharmaceuticals, antibodies or vaccines.

Vegetable or seed oils are the major source of energy and nutrition inhuman and animal diet. They are also used for the production ofindustrial products, such as paints, inks and lubricants. In addition,plant oils represent renewable sources of long-chain hydrocarbons, whichcan be used as fuel. Since the currently used fossil fuels are finiteresources and are gradually being depleted, fast growing biomass cropsmay be used as alternative fuels or for energy feedstocks and may reducethe dependence on fossil energy supplies. However, the major bottleneckfor increasing consumption of plant oils as bio-fuel is the oil price,which is still higher than fossil fuel. In addition, the production rateof plant oil is limited by the availability of agricultural land andwater. Thus, increasing plant oil yields from the same growing area caneffectively overcome the shortage in production space and can decreasevegetable oil prices at the same time.

Studies aiming at increasing plant oil yields focus on theidentification of genes involved in oil metabolism as well as in genescapable of increasing plant and seed yields in transgenic plants. Genesknown to be involved in increasing plant oil yields include thoseparticipating in fatty acid synthesis or sequestering such as desaturase[e.g., DELTA6, DELTA12 or acyl-ACP (Ssi2; Arabidopsis InformationResource (TAIR; arabidopsis (dot) org/), TAIR No. AT2G43710)], OleosinA(TAIR No. AT3G01570) or FAD3 (TAIR No. AT2G29980), and varioustranscription factors and activators such as Lec1 [TAIR No. AT1G21970,Lotan et al. 1998. Cell. 26; 93(7):1195-205], Lec2 [TAIR No. AT1G28300,Santos Mendoza et al. 2005, FEBS Lett. 579(21):4666-70], Fus3 (TAIR No.AT3G26790), ABI3 [TAIR No. AT3G24650, Lara et al. 2003. J Biol Chem.278(23): 21003-11] and Wri1 [TAIR No. AT3G54320, Cernac and Benning,2004. Plant J. 40(4): 575-85].

Genetic engineering efforts aiming at increasing oil content in plants(e.g., in seeds) include upregulating endoplasmic reticulum (FAD3) andplastidal (FAD7) fatty acid desaturases in potato (Zabrouskov V., etal., 2002; Physiol Plant. 116:172-185); over-expressing the GmDof4 andGmDof11 transcription factors (Wang H W et al., 2007; Plant J.52:716-29); over-expressing a yeast glycerol-3-phosphate dehydrogenaseunder the control of a seed-specific promoter (Vigeolas H, et al. 2007,Plant Biotechnol J. 5:431-41; U.S. Pat. Appl. No. 20060168684); usingArabidopsis FAE1 and yeast SLC1-1 genes for improvements in erucic acidand oil content in rapeseed (Katavic V, et al., 2000, Biochem Soc Trans.28:935-7).

Various patent applications disclose genes and proteins which canincrease oil content in plants. These include for example, U.S. Pat.Appl. No. 20080076179 (lipid metabolism protein); U.S. Pat. Appl. No.20060206961 (the Ypr140w polypeptide); U.S. Pat. Appl. No. 20060174373[triacylglycerols synthesis enhancing protein (TEP)]; U.S. Pat. Appl.Nos. 20070169219, 20070006345, 20070006346 and 20060195943 (disclosetransgenic plants with improved nitrogen use efficiency which can beused for the conversion into fuel or chemical feedstocks); WO2008/122980(polynucleotides for increasing oil content, growth rate, biomass, yieldand/or vigor of a plant).

A common approach to promote plant growth has been, and continues to be,the use of natural as well as synthetic nutrients (fertilizers). Thus,fertilizers are the fuel behind the “green revolution”, directlyresponsible for the exceptional increase in crop yields during the last40 years, and are considered the number one overhead expense inagriculture. For example, inorganic nitrogenous fertilizers such asammonium nitrate, potassium nitrate, or urea, typically accounts for 40%of the costs associated with crops such as corn and wheat. Of the threemacronutrients provided as main fertilizers [Nitrogen (N), Phosphate (P)and Potassium (K)], nitrogen is often the rate-limiting element in plantgrowth and all field crops have a fundamental dependence on inorganicnitrogenous fertilizer. Nitrogen is responsible for biosynthesis ofamino and nucleic acids, prosthetic groups, plant hormones, plantchemical defenses, etc. and usually needs to be replenished every year,particularly for cereals, which comprise more than half of thecultivated areas worldwide. Thus, nitrogen is translocated to the shoot,where it is stored in the leaves and stalk during the rapid step ofplant development and up until flowering. In corn for example, plantsaccumulate the bulk of their organic nitrogen during the period of graingermination, and until flowering. Once fertilization of the plant hasoccurred, grains begin to form and become the main sink of plantnitrogen. The stored nitrogen can be then redistributed from the leavesand stalk that served as storage compartments until grain formation.

Since fertilizer is rapidly depleted from most soil types, it must besupplied to growing crops two or three times during the growing season.In addition, the low nitrogen use efficiency (NUE) of the main crops(e.g., in the range of only 30-70%) negatively affects the inputexpenses for the farmer, due to the excess fertilizer applied. Moreover,the over and inefficient use of fertilizers are major factorsresponsible for environmental problems such as eutrophication ofgroundwater, lakes, rivers and seas, nitrate pollution in drinking waterwhich can cause methemoglobinemia, phosphate pollution, atmosphericpollution and the like. However, in spite of the negative impact offertilizers on the environment, and the limits on fertilizer use, whichhave been legislated in several countries, the use of fertilizers isexpected to increase in order to support food and fiber production forrapid population growth on limited land resources. For example, it hasbeen estimated that by 2050, more than 150 million tons of nitrogenousfertilizer will be used worldwide annually.

Increased use efficiency of nitrogen by plants should enable crops to becultivated with lower fertilizer input, or alternatively to becultivated on soils of poorer quality and would therefore havesignificant economic impact in both developed and developingagricultural systems.

Genetic improvement of fertilizer use efficiency (FUE) in plants can begenerated either via traditional breeding or via genetic engineering.

Attempts to generate plants with increased FUE have been described inU.S. Pat. Appl. Publication No. 20020046419 (U.S. Pat. No. 7,262,055 toChoo, et al.); U.S. Pat. Appl. No. 20050108791 to Edgerton et al.; U.S.Pat. Appl. No. 20060179511 to Chomet et al.; Good, A, et al. 2007(Engineering nitrogen use efficiency with alanine aminotransferase.Canadian Journal of Botany 85: 252-262); and Good A G et al. 2004(Trends Plant Sci. 9:597-605).

Yanagisawa et al. (Proc. Natl. Acad. Sci. U.S.A. 2004 101:7833-8)describe Dof1 transgenic plants which exhibit improved growth underlow-nitrogen conditions.

U.S. Pat. No. 6,084,153 to Good et al. discloses the use of a stressresponsive promoter to control the expression of Alanine AmineTransferase (AlaAT) and transgenic canola plants with improved droughtand nitrogen deficiency tolerance when compared to control plants.

Abiotic stress (ABS; also referred to as “environmental stress”)conditions such as salinity, drought, flood, suboptimal temperature andtoxic chemical pollution, cause substantial damage to agriculturalplants. Most plants have evolved strategies to protect themselvesagainst these conditions. However, if the severity and duration of thestress conditions are too great, the effects on plant development,growth and yield of most crop plants are profound. Furthermore, most ofthe crop plants are highly susceptible to abiotic stress and thusnecessitate optimal growth conditions for commercial crop yields.Continuous exposure to stress causes major alterations in the plantmetabolism which ultimately leads to cell death and consequently yieldlosses.

Drought is a gradual phenomenon, which involves periods of abnormallydry weather that persists long enough to produce serious hydrologicimbalances such as crop damage, water supply shortage and increasedsusceptibility to various diseases. In severe cases, drought can lastmany years and results in devastating effects on agriculture and watersupplies. Furthermore, drought is associated with increasesusceptibility to various diseases.

For most crop plants, the land regions of the world are too arid. Inaddition, overuse of available water results in increased loss ofagriculturally-usable land (desertification), and increase of saltaccumulation in soils adds to the loss of available water in soils.

Salinity, high salt levels, affects one in five hectares of irrigatedland. None of the top five food crops, i.e., wheat, corn, rice,potatoes, and soybean, can tolerate excessive salt. Detrimental effectsof salt on plants result from both water deficit, which leads to osmoticstress (similar to drought stress), and the effect of excess sodium ionson critical biochemical processes. As with freezing and drought, highsalt causes water deficit; and the presence of high salt makes itdifficult for plant roots to extract water from their environment. Soilsalinity is thus one of the more important variables that determinewhether a plant may thrive. In many parts of the world, sizable landareas are uncultivable due to naturally high soil salinity. Thus,salination of soils that are used for agricultural production is asignificant and increasing problem in regions that rely heavily onagriculture, and is worsen by over-utilization, over-fertilization andwater shortage, typically caused by climatic change and the demands ofincreasing population. Salt tolerance is of particular importance earlyin a plant's lifecycle, since evaporation from the soil surface causesupward water movement, and salt accumulates in the upper soil layerwhere the seeds are placed. On the other hand, germination normallytakes place at a salt concentration which is higher than the mean saltlevel in the whole soil profile.

Salt and drought stress signal transduction consist of ionic and osmotichomeostasis signaling pathways. The ionic aspect of salt stress issignaled via the SOS pathway where a calcium-responsive SOS3-SOS2protein kinase complex controls the expression and activity of iontransporters such as SOS1. The osmotic component of salt stress involvescomplex plant reactions that overlap with drought and/or cold stressresponses.

Suboptimal temperatures affect plant growth and development through thewhole plant life cycle. Thus, low temperatures reduce germination rateand high temperatures result in leaf necrosis. In addition, matureplants that are exposed to excess of heat may experience heat shock,which may arise in various organs, including leaves and particularlyfruit, when transpiration is insufficient to overcome heat stress. Heatalso damages cellular structures, including organelles and cytoskeleton,and impairs membrane function. Heat shock may produce a decrease inoverall protein synthesis, accompanied by expression of heat shockproteins, e.g., chaperones, which are involved in refolding proteinsdenatured by heat. High-temperature damage to pollen almost alwaysoccurs in conjunction with drought stress, and rarely occurs underwell-watered conditions. Combined stress can alter plant metabolism innovel ways. Excessive chilling conditions, e.g., low, but abovefreezing, temperatures affect crops of tropical origins, such assoybean, rice, maize, and cotton. Typical chilling damage includeswilting, necrosis, chlorosis or leakage of ions from cell membranes. Theunderlying mechanisms of chilling sensitivity are not completelyunderstood yet, but probably involve the level of membrane saturationand other physiological deficiencies. Excessive light conditions, whichoccur under clear atmospheric conditions subsequent to cold latesummer/autumn nights, can lead to photoinhibition of photosynthesis(disruption of photosynthesis). In addition, chilling may lead to yieldlosses and lower product quality through the delayed ripening of maize.

Common aspects of drought, cold and salt stress response [Reviewed inXiong and Zhu (2002) Plant Cell Environ. 25: 131-139] include: (a)transient changes in the cytoplasmic calcium levels early in thesignaling event; (b) signal transduction via mitogen-activated and/orcalcium dependent protein kinases (CDPKs) and protein phosphatases; (c)increases in abscisic acid levels in response to stress triggering asubset of responses; (d) inositol phosphates as signal molecules (atleast for a subset of the stress responsive transcriptional changes; (e)activation of phospholipases which in turn generates a diverse array ofsecond messenger molecules, some of which might regulate the activity ofstress responsive kinases; (f) induction of late embryogenesis abundant(LEA) type genes including the CRT/DRE responsive COR/RD genes; (g)increased levels of antioxidants and compatible osmolytes such asproline and soluble sugars; and (h) accumulation of reactive oxygenspecies such as superoxide, hydrogen peroxide, and hydroxyl radicals.Abscisic acid biosynthesis is regulated by osmotic stress at multiplesteps. Both ABA-dependent and -independent osmotic stress signalingfirst modify constitutively expressed transcription factors, leading tothe expression of early response transcriptional activators, which thenactivate downstream stress tolerance effector genes.

Several genes which increase tolerance to cold or salt stress can alsoimprove drought stress protection, these include for example, thetranscription factor AtCBF/DREB1, OsCDPK7 (Saijo et al. 2000, Plant J.23: 319-327) or AVP1 (a vacuolar pyrophosphatase-proton pump, Gaxiola etal. 2001, Proc. Natl. Acad. Sci. USA 98: 11444-11449).

Studies have shown that plant adaptations to adverse environmentalconditions are complex genetic traits with polygenic nature.Conventional means for crop and horticultural improvements utilizeselective breeding techniques to identify plants having desirablecharacteristics. However, selective breeding is tedious, time consumingand has an unpredictable outcome. Furthermore, limited germplasmresources for yield improvement and incompatibility in crosses betweendistantly related plant species represent significant problemsencountered in conventional breeding. Advances in genetic engineeringhave allowed mankind to modify the germplasm of plants by expression ofgenes-of-interest in plants. Such a technology has the capacity togenerate crops or plants with improved economic, agronomic orhorticultural traits.

Genetic engineering efforts, aimed at conferring abiotic stresstolerance to transgenic crops, have been described in variouspublications [Apse and Blumwald (Curr Opin Biotechnol. 13:146-150,2002), Quesada et al. (Plant Physiol. 130:951-963, 2002), Holmström etal. (Nature 379: 683-684, 1996), Xu et al. (Plant Physiol 110: 249-257,1996), Pilon-Smits and Ebskamp (Plant Physiol 107: 125-130, 1995) andTarczynski et al. (Science 259: 508-510, 1993)].

Various patents and patent applications disclose genes and proteinswhich can be used for increasing tolerance of plants to abioticstresses. These include for example, U.S. Pat. Nos. 5,296,462 and5,356,816 (for increasing tolerance to cold stress); U.S. Pat. No.6,670,528 (for increasing ABST); U.S. Pat. No. 6,720,477 (for increasingABST); U.S. application Ser. Nos. 09/938,842 and 10/342,224 (forincreasing ABST); U.S. application Ser. No. 10/231,035 (for increasingABST); WO2004/104162 (for increasing ABST and biomass); WO2007/020638(for increasing ABST, biomass, vigor and/or yield); WO2007/049275 (forincreasing ABST, biomass, vigor and/or yield); WO2010/076756 (forincreasing ABST, biomass and/or yield). WO2009/083958 (for increasingwater use efficiency, fertilizer use efficiency, biotic/abiotic stresstolerance, yield and/or biomass); WO2010/020941 (for increasing nitrogenuse efficiency, abiotic stress tolerance, yield and/or biomass);WO2009/141824 (for increasing plant utility); WO2010/049897 (forincreasing plant yield).

Nutrient deficiencies cause adaptations of the root architecture,particularly notably for example is the root proliferation withinnutrient rich patches to increase nutrient uptake. Nutrient deficienciescause also the activation of plant metabolic pathways which maximize theabsorption, assimilation and distribution processes such as byactivating architectural changes. Engineering the expression of thetriggered genes may cause the plant to exhibit the architectural changesand enhanced metabolism also under other conditions.

In addition, it is widely known that the plants usually respond to waterdeficiency by creating a deeper root system that allows access tomoisture located in deeper soil layers. Triggering this effect willallow the plants to access nutrients and water located in deeper soilhorizons particularly those readily dissolved in water like nitrates.

Cotton and cotton by-products provide raw materials that are used toproduce a wealth of consumer-based products in addition to textilesincluding cotton foodstuffs, livestock feed, fertilizer and paper. Theproduction, marketing, consumption and trade of cotton-based productsgenerate an excess of $100 billion annually in the U.S. alone, makingcotton the number one value-added crop.

Even though 90% of cotton's value as a crop resides in the fiber (lint),yield and fiber quality has declined due to general erosion in geneticdiversity of cotton varieties, and an increased vulnerability of thecrop to environmental conditions.

There are many varieties of cotton plant, from which cotton fibers witha range of characteristics can be obtained and used for variousapplications. Cotton fibers may be characterized according to a varietyof properties, some of which are considered highly desirable within thetextile industry for the production of increasingly high qualityproducts and optimal exploitation of modem spinning technologies.Commercially desirable properties include length, length uniformity,fineness, maturity ratio, decreased fuzz fiber production, micronaire,bundle strength, and single fiber strength. Much effort has been putinto the improvement of the characteristics of cotton fibers mainlyfocusing on fiber length and fiber fineness. In particular, there is agreat demand for cotton fibers of specific lengths.

A cotton fiber is composed of a single cell that has differentiated froman epidermal cell of the seed coat, developing through four stages,i.e., initiation, elongation, secondary cell wall thickening andmaturation stages. More specifically, the elongation of a cotton fibercommences in the epidermal cell of the ovule immediately followingflowering, after which the cotton fiber rapidly elongates forapproximately 21 days. Fiber elongation is then terminated, and asecondary cell wall is formed and grown through maturation to become amature cotton fiber.

Several candidate genes which are associated with the elongation,formation, quality and yield of cotton fibers were disclosed in variouspatent applications such as U.S. Pat. No. 5,880,100 and U.S. patentapplication Ser. Nos. 08/580,545, 08/867,484 and 09/262,653 (describinggenes involved in cotton fiber elongation stage); WO0245485 (improvingfiber quality by modulating sucrose synthase); U.S. Pat. No. 6,472,588and WO0117333 (increasing fiber quality by transformation with a DNAencoding sucrose phosphate synthase); WO9508914 (using a fiber-specificpromoter and a coding sequence encoding cotton peroxidase); WO9626639(using an ovary specific promoter sequence to express plant growthmodifying hormones in cotton ovule tissue, for altering fiber qualitycharacteristics such as fiber dimension and strength); U.S. Pat. No.5,981,834, U.S. Pat. No. 5,597,718, U.S. Pat. No. 5,620,882, U.S. Pat.No. 5,521,708 and U.S. Pat. No. 5,495,070 (coding sequences to alter thefiber characteristics of transgenic fiber producing plants); U.S. patentapplications U.S. 2002049999 and U.S. 2003074697 (expressing a genecoding for endoxyloglucan transferase, catalase or peroxidase forimproving cotton fiber characteristics); WO 01/40250 (improving cottonfiber quality by modulating transcription factor gene expression); WO96/40924 (a cotton fiber transcriptional initiation regulatory regionassociated which is expressed in cotton fiber); EP0834566 (a gene whichcontrols the fiber formation mechanism in cotton plant); WO2005/121364(improving cotton fiber quality by modulating gene expression);WO2008/075364 (improving fiber quality, yield/biomass/vigor and/orabiotic stress tolerance of plants).

WO publication No. 2004/104162 discloses methods of increasing abioticstress tolerance and/or biomass in plants and plants generated thereby.

WO publication No. 2004/111183 discloses nucleotide sequences forregulating gene expression in plant trichomes and constructs and methodsutilizing same.

WO publication No. 2004/081173 discloses novel plant derived regulatorysequences and constructs and methods of using such sequences fordirecting expression of exogenous polynucleotide sequences in plants.

WO publication No. 2005/121364 discloses polynucleotides andpolypeptides involved in plant fiber development and methods of usingsame for improving fiber quality, yield and/or biomass of a fiberproducing plant.

WO publication No. 2007/049275 discloses isolated polypeptides,polynucleotides encoding same, transgenic plants expressing same andmethods of using same for increasing fertilizer use efficiency, plantabiotic stress tolerance and biomass.

WO publication No. 2007/020638 discloses methods of increasing abioticstress tolerance and/or biomass in plants and plants generated thereby.

WO publication No. 2008/122980 discloses genes constructs and methodsfor increasing oil content, growth rate and biomass of plants.

WO publication No. 2008/075364 discloses polynucleotides involved inplant fiber development and methods of using same.

WO publication No. 2009/083958 discloses methods of increasing water useefficiency, fertilizer use efficiency, biotic/abiotic stress tolerance,yield and biomass in plant and plants generated thereby.

WO publication No. 2009/141824 discloses isolated polynucleotides andmethods using same for increasing plant utility.

WO publication No. 2009/013750 discloses genes, constructs and methodsof increasing abiotic stress tolerance, biomass and/or yield in plantsgenerated thereby.

WO publication No. 2010/020941 discloses methods of increasing nitrogenuse efficiency, abiotic stress tolerance, yield and biomass in plantsand plants generated thereby.

WO publication No. 2010/076756 discloses isolated polynucleotides forincreasing abiotic stress tolerance, yield, biomass, growth rate, vigor,oil content, fiber yield, fiber quality, and/or nitrogen use efficiencyof a plant.

WO2010/100595 publication discloses isolated polynucleotides andpolypeptides, and methods of using same for increasing plant yieldand/or agricultural characteristics.

WO publication No. 2010/049897 discloses isolated polynucleotides andpolypeptides and methods of using same for increasing plant yield,biomass, growth rate, vigor, oil content, abiotic stress tolerance ofplants and nitrogen use efficiency.

WO2010/143138 publication discloses isolated polynucleotides andpolypeptides, and methods of using same for increasing nitrogen useefficiency, fertilizer use efficiency, yield, growth rate, vigor,biomass, oil content, abiotic stress tolerance and/or water useefficiency.

WO publication No. 2011/080674 discloses isolated polynucleotides andpolypeptides and methods of using same for increasing plant yield,biomass, growth rate, vigor, oil content, abiotic stress tolerance ofplants and nitrogen use efficiency.

WO2011/015985 publication discloses polynucleotides and polypeptides forincreasing desirable plant qualities.

WO2011/135527 publication discloses isolated polynucleotides andpolypeptides for increasing plant yield and/or agriculturalcharacteristics.

WO2012/028993 publication discloses isolated polynucleotides andpolypeptides, and methods of using same for increasing nitrogen useefficiency, yield, growth rate, vigor, biomass, oil content, and/orabiotic stress tolerance.

WO2012/085862 publication discloses isolated polynucleotides andpolypeptides, and methods of using same for improving plant properties.

WO2012/150598 publication discloses isolated polynucleotides andpolypeptides and methods of using same for increasing plant yield,biomass, growth rate, vigor, oil content, abiotic stress tolerance ofplants and nitrogen use efficiency.

WO2013/027223 publication discloses isolated polynucleotides andpolypeptides, and methods of using same for increasing plant yieldand/or agricultural characteristics.

WO2013/080203 publication discloses isolated polynucleotides andpolypeptides, and methods of using same for increasing nitrogen useefficiency, yield, growth rate, vigor, biomass, oil content, and/orabiotic stress tolerance.

WO2013/098819 publication discloses isolated polynucleotides andpolypeptides, and methods of using same for increasing yield of plants.

WO2013/128448 publication discloses isolated polynucleotides andpolypeptides and methods of using same for increasing plant yield,biomass, growth rate, vigor, oil content, abiotic stress tolerance ofplants and nitrogen use efficiency.

WO 2013/179211 publication discloses isolated polynucleotides andpolypeptides, and methods of using same for increasing plant yieldand/or agricultural characteristics.

SUMMARY OF THE INVENTION

According to an aspect of some embodiments of the present inventionthere is provided a method of increasing yield, growth rate, biomass,vigor, oil content, seed yield, fiber yield, fiber quality, fiberlength, photosynthetic capacity, nitrogen use efficiency, and/or abioticstress tolerance of a plant, comprising expressing within the plant anexogenous polynucleotide comprising a nucleic acid sequence encoding apolypeptide at least 80% identical to SEQ ID NO: 713-716, 718-734,737-741, 743-744, 746-765, 767-784, 786-788, 790-795, 797, 810-811,813-876, 878-889, 891-929, 931-1021, 1029-1064, 1067-1074, 1076-1080,1082-1088, 1091-1092, 1094-1153, 9283-9526, 9536, 9550-9772, 9825, 9832,9843-9881, 9899, 9908, 9925-9988, 9990-10284, 10290-11275, 11278-11279,11282-11284, 11289-11295, 11297-11299, 11301, 11303-11305, 11308-11312,11314, 11384, 11386, 11394, 11400, 11407, 11416-11417, 11421,11425-11426, 11429, 11433, 11439-11441, 11443-11444, 11446-11447,11449-11450, 11453-11455, 11457, 11460, 11468-11469, 11471, 11475,11482, 11485, 11488, 11494-11496, 11500-11503, 11505-11506, 11510-11513,11516-11525, 11530, 11551, 11555, 11559, 11561, 11570-11571, 11582,11589, 11605, 11612, 11695, 11697, 11699-13027, 13057, 13066,13091-13092, 13104, 13109, 13116, 13119-13180, 13188, 13192-13327,13329-13352, 13355-13929, 13941-13942, 13946-14913, 14989-15034,15037-15049, 15051-15072, 15074-15221, 15229-15252, 15254-15272,15281-15409, 15425, 15428-15434, 15455-15721 or 15722, therebyincreasing the yield, growth rate, biomass, vigor, oil content, seedyield, fiber yield, fiber quality, fiber length, photosyntheticcapacity, nitrogen use efficiency, and/or abiotic stress tolerance ofthe plant.

According to an aspect of some embodiments of the present inventionthere is provided a method of increasing yield, growth rate, biomass,vigor, oil content, seed yield, fiber yield, fiber quality, fiberlength, photosynthetic capacity, nitrogen use efficiency, and/or abioticstress tolerance of a plant, comprising expressing within the plant anexogenous polynucleotide comprising a nucleic acid sequence encoding apolypeptide selected from the group consisting of SEQ ID NOs: 713-735,737-741, 743-765, 767-795, 797, 809-1021, 1029-1064, 1067-1080,1082-1092, 1094-1153, 9276-9281, 9283-9532, 9534-9541, 9543-9545,9548-9774, 9776, 9778-9785, 9788-9791, 9793-9801, 9803, 9806-9807,9809-9820, 9822-9823, 9825-9838, 9840-9841, 9843-9881, 9889-9890,9893-9894, 9897-9899, 9901, 9904, 9906, 9908-9910, 9912-10285,10287-11276, 11278-11319, 11321, 11323, 11328-11330, 11333-11336,11339-11342, 11344-11355, 11357, 11359-11362, 11364-11366, 11369-13113,13115-13944, 13946-14913, 14915, 14917-14918, 14920-14921, 14923-14924,14927-14933, 14937, 14939-14940, 14942, 14944-14949, 14951, 14953,14955-14958, 14960-14962, 14964-14971, 14973, 14976, 14978-14979,14989-15221, 15225-15272, 15275-15410, 15412-15420, 15422-15423,15425-15426, 15428-15434, 15436, 15440-15441, 15443-15444, 15446,15448-15449, and 15451-15726, thereby increasing the yield, growth rate,biomass, vigor, oil content, seed yield, fiber yield, fiber quality,fiber length, photosynthetic capacity, nitrogen use efficiency, and/orabiotic stress tolerance of the plant.

According to an aspect of some embodiments of the present inventionthere is provided a method of producing a crop comprising growing a cropplant transformed with an exogenous polynucleotide comprising a nucleicacid sequence encoding a polypeptide at least 80% homologous to theamino acid sequence selected from the group consisting of SEQ ID NOs:713-716, 718-734, 737-741, 743-744, 746-765, 767-784, 786-788, 790-795,797, 810-811, 813-876, 878-889, 891-929, 931-1021, 1029-1064, 1067-1074,1076-1080, 1082-1088, 1091-1092, 1094-1153, 9283-9526, 9536, 9550-9772,9825, 9832, 9843-9881, 9899, 9908, 9925-9988, 9990-10284, 10290-11275,11278-11279, 11282-11284, 11289-11295, 11297-11299, 11301, 11303-11305,11308-11312, 11314, 11384, 11386, 11394, 11400, 11407, 11416-11417,11421, 11425-11426, 11429, 11433, 11439-11441, 11443-11444, 11446-11447,11449-11450, 11453-11455, 11457, 11460, 11468-11469, 11471, 11475,11482, 11485, 11488, 11494-11496, 11500-11503, 11505-11506, 11510-11513,11516-11525, 11530, 11551, 11555, 11559, 11561, 11570-11571, 11582,11589, 11605, 11612, 11695, 11697, 11699-13027, 13057, 13066,13091-13092, 13104, 13109, 13116, 13119-13180, 13188, 13192-13327,13329-13352, 13355-13929, 13941-13942, 13946-14913, 14989-15034,15037-15049, 15051-15072, 15074-15221, 15229-15252, 15254-15272,15281-15409, 15425, 15428-15434, and 15455-15722, wherein the crop plantis derived from plants which have been transformed with the exogenouspolynucleotide and which have been selected for increased yield,increased growth rate, increased biomass, increased vigor, increased oilcontent, increased seed yield, increased fiber yield, increased fiberquality, increased fiber length, increased photosynthetic capacity,increased nitrogen use efficiency, and/or increased abiotic stresstolerance as compared to a wild type plant of the same species which isgrown under the same growth conditions, and the crop plant having theincreased yield, increased growth rate, increased biomass, increasedvigor, increased oil content, increased seed yield, increased fiberyield, increased fiber quality, increased fiber length, increasedphotosynthetic capacity, increased nitrogen use efficiency, and/orincreased abiotic stress tolerance, thereby producing the crop.

According to an aspect of some embodiments of the present inventionthere is provided a method of increasing yield, growth rate, biomass,vigor, oil content, seed yield, fiber yield, fiber quality, fiberlength, photosynthetic capacity, nitrogen use efficiency, and/or abioticstress tolerance of a plant, comprising expressing within the plant anexogenous polynucleotide comprising a nucleic acid sequence at least 80%identical to SEQ ID NO: 4-7, 9-25, 28-32, 34-35, 37-56, 58-75, 77-79,81-86, 88, 101-102, 104-167, 169-180, 182-220, 222-312, 320-389, 391,395-398, 400-416, 419-423, 425-426, 428-447, 449-464, 466-468, 470-475,477, 490-491, 493-555, 557-568, 570-605, 607-696, 704-709, 1164-1439,1453, 1468-1733, 1788, 1795, 1806-1860, 1884, 1899, 1917-2324,2331-3501, 3504-3506, 3509-3511, 3518-3526, 3528-3530, 3532, 3534-3536,3540-3547, 3549, 3638, 3641-3643, 3652, 3661, 3663, 3668, 3671,3683-3684, 3689, 3695-3696, 3700-3702, 3708, 3715-3718, 3720-3721,3723-3724, 3726-3727, 3732-3733, 3735, 3737, 3740, 3750-3751, 3753,3757, 3764-3765, 3768, 3772, 3776, 3783-3785, 3789-3792, 3794-3795,3800-3803, 3806-3818, 3827, 3889, 3894, 3898, 3900, 3915-3916, 3936,3943, 3964, 3971, 4099, 4101, 4103-4245, 4247-6064, 6103, 6112,6137-6138, 6150, 6155, 6162, 6165-6237, 6245, 6249-6406, 6408-6434,6437-7124, 7140-7141, 7145-8305, 8387-8453, 8457-8472, 8474-8505,8507-8683, 8691-8720, 8722-8748, 8757-8898, 8915, 8918-8927, 8948-9270or 9271, thereby increasing the yield, growth rate, biomass, vigor, oilcontent, seed yield, fiber yield, fiber quality, fiber length,photosynthetic capacity, nitrogen use efficiency, and/or abiotic stresstolerance of the plant.

According to an aspect of some embodiments of the present inventionthere is provided a method of increasing yield, growth rate, biomass,vigor, oil content, seed yield, fiber yield, fiber quality, fiberlength, photosynthetic capacity, nitrogen use efficiency, and/or abioticstress tolerance of a plant, comprising expressing within the plant anexogenous polynucleotide comprising the nucleic acid sequence selectedfrom the group consisting of SEQ ID NOs: 4-86, 88, 100-312, 320-389,391, 395-475, 477, 489-696, 704-709, 1157-4245, 4247-8375, 8387-8683,and 8686-9275, thereby increasing the yield, growth rate, biomass,vigor, oil content, seed yield, fiber yield, fiber quality, fiberlength, photosynthetic capacity, nitrogen use efficiency, and/or abioticstress tolerance of the plant.

According to an aspect of some embodiments of the present inventionthere is provided a method of producing a crop comprising growing a cropplant transformed with an exogenous polynucleotide which comprises anucleic acid sequence which is at least 80% identical to the nucleicacid sequence selected from the group consisting of SEQ ID NOs: 4-7,9-25, 28-32, 34-35, 37-56, 58-75, 77-79, 81-86, 88, 101-102, 104-167,169-180, 182-220, 222-312, 320-389, 391, 395-398, 400-416, 419-423,425-426, 428-447, 449-464, 466-468, 470-475, 477, 490-491, 493-555,557-568, 570-605, 607-696, 704-709, 1164-1439, 1453, 1468-1733, 1788,1795, 1806-1860, 1884, 1899, 1917-2324, 2331-3501, 3504-3506, 3509-3511,3518-3526, 3528-3530, 3532, 3534-3536, 3540-3547, 3549, 3638, 3641-3643,3652, 3661, 3663, 3668, 3671, 3683-3684, 3689, 3695-3696, 3700-3702,3708, 3715-3718, 3720-3721, 3723-3724, 3726-3727, 3732-3733, 3735, 3737,3740, 3750-3751, 3753, 3757, 3764-3765, 3768, 3772, 3776, 3783-3785,3789-3792, 3794-3795, 3800-3803, 3806-3818, 3827, 3889, 3894, 3898,3900, 3915-3916, 3936, 3943, 3964, 3971, 4099, 4101, 4103-4245,4247-6064, 6103, 6112, 6137-6138, 6150, 6155, 6162, 6165-6237, 6245,6249-6406, 6408-6434, 6437-7124, 7140-7141, 7145-8305, 8387-8453,8457-8472, 8474-8505, 8507-8683, 8691-8720, 8722-8748, 8757-8898, 8915,8918-8927, and 8948-9271, wherein the crop plant is derived from plantswhich have been transformed with the exogenous polynucleotide and whichhave been selected for increased yield, increased growth rate, increasedbiomass, increased vigor, increased oil content, increased seed yield,increased fiber yield, increased fiber quality, increased fiber length,increased photosynthetic capacity, increased nitrogen use efficiency,and/or increased abiotic stress tolerance as compared to a wild typeplant of the same species which is grown under the same growthconditions, and the crop plant having the increased yield, increasedgrowth rate, increased biomass, increased vigor, increased oil content,increased seed yield, increased fiber yield, increased fiber quality,increased fiber length, increased photosynthetic capacity, increasednitrogen use efficiency, and/or increased abiotic stress tolerance,thereby producing the crop.

According to an aspect of some embodiments of the present inventionthere is provided an isolated polynucleotide comprising a nucleic acidsequence encoding a polypeptide which comprises an amino acid sequenceat least 80% homologous to the amino acid sequence set forth in SEQ IDNO: 713-716, 718-734, 737-741, 743-744, 746-765, 767-784, 786-788,790-795, 797, 810-811, 813-876, 878-889, 891-929, 931-1021, 1029-1064,1067-1074, 1076-1080, 1082-1088, 1091-1092, 1094-1153, 9283-9526, 9536,9550-9772, 9825, 9832, 9843-9881, 9899, 9908, 9925-9988, 9990-10284,10290-11275, 11278-11279, 11282-11284, 11289-11295, 11297-11299, 11301,11303-11305, 11308-11312, 11314, 11384, 11386, 11394, 11400, 11407,11416-11417, 11421, 11425-11426, 11429, 11433, 11439-11441, 11443-11444,11446-11447, 11449-11450, 11453-11455, 11457, 11460, 11468-11469, 11471,11475, 11482, 11485, 11488, 11494-11496, 11500-11503, 11505-11506,11510-11513, 11516-11525, 11530, 11551, 11555, 11559, 11561,11570-11571, 11582, 11589, 11605, 11612, 11695, 11697, 11699-13027,13057, 13066, 13091-13092, 13104, 13109, 13116, 13119-13180, 13188,13192-13327, 13329-13352, 13355-13929, 13941-13942, 13946-14913,14989-15034, 15037-15049, 15051-15072, 15074-15221, 15229-15252,15254-15272, 15281-15409, 15425, 15428-15434, 15455-15721 or 15722,wherein the amino acid sequence is capable of increasing yield, growthrate, biomass, vigor, oil content, seed yield, fiber yield, fiberquality, fiber length, photosynthetic capacity, nitrogen use efficiency,and/or abiotic stress tolerance of a plant.

According to an aspect of some embodiments of the present inventionthere is provided an isolated polynucleotide comprising a nucleic acidsequence encoding a polypeptide which comprises the amino acid sequenceselected from the group consisting of SEQ ID NOs: 713-735, 737-741,743-765, 767-795, 797, 809-1021, 1029-1064, 1067-1080, 1082-1092,1094-1153, 9276-9281, 9283-9532, 9534-9541, 9543-9545, 9548-9774, 9776,9778-9785, 9788-9791, 9793-9801, 9803, 9806-9807, 9809-9820, 9822-9823,9825-9838, 9840-9841, 9843-9881, 9889-9890, 9893-9894, 9897-9899, 9901,9904, 9906, 9908-9910, 9912-10285, 10287-11276, 11278-11319, 11321,11323, 11328-11330, 11333-11336, 11339-11342, 11344-11355, 11357,11359-11362, 11364-11366, 11369-13113, 13115-13944, 13946-14913, 14915,14917-14918, 14920-14921, 14923-14924, 14927-14933, 14937, 14939-14940,14942, 14944-14949, 14951, 14953, 14955-14958, 14960-14962, 14964-14971,14973, 14976, 14978-14979, 14989-15221, 15225-15272, 15275-15410,15412-15420, 15422-15423, 15425-15426, 15428-15434, 15436, 15440-15441,15443-15444, 15446, 15448-15449, and 15451-15726.

According to an aspect of some embodiments of the present inventionthere is provided an isolated polynucleotide comprising a nucleic acidsequence at least 80% identical to SEQ ID NO: 4-7, 9-25, 28-32, 34-35,37-56, 58-75, 77-79, 81-86, 88, 101-102, 104-167, 169-180, 182-220,222-312, 320-389, 391, 395-398, 400-416, 419-423, 425-426, 428-447,449-464, 466-468, 470-475, 477, 490-491, 493-555, 557-568, 570-605,607-696, 704-709, 1164-1439, 1453, 1468-1733, 1788, 1795, 1806-1860,1884, 1899, 1917-2324, 2331-3501, 3504-3506, 3509-3511, 3518-3526,3528-3530, 3532, 3534-3536, 3540-3547, 3549, 3638, 3641-3643, 3652,3661, 3663, 3668, 3671, 3683-3684, 3689, 3695-3696, 3700-3702, 3708,3715-3718, 3720-3721, 3723-3724, 3726-3727, 3732-3733, 3735, 3737, 3740,3750-3751, 3753, 3757, 3764-3765, 3768, 3772, 3776, 3783-3785,3789-3792, 3794-3795, 3800-3803, 3806-3818, 3827, 3889, 3894, 3898,3900, 3915-3916, 3936, 3943, 3964, 3971, 4099, 4101, 4103-4245,4247-6064, 6103, 6112, 6137-6138, 6150, 6155, 6162, 6165-6237, 6245,6249-6406, 6408-6434, 6437-7124, 7140-7141, 7145-8305, 8387-8453,8457-8472, 8474-8505, 8507-8683, 8691-8720, 8722-8748, 8757-8898, 8915,8918-8927, 8948-9270 or 9271, wherein the nucleic acid sequence iscapable of increasing yield, growth rate, biomass, vigor, oil content,seed yield, fiber yield, fiber quality, fiber length, photosyntheticcapacity, nitrogen use efficiency, and/or abiotic stress tolerance of aplant.

According to an aspect of some embodiments of the present inventionthere is provided an isolated polynucleotide comprising the nucleic acidsequence selected from the group consisting of SEQ ID NOs: 4-86, 88,100-312, 320-389, 391, 395-475, 477, 489-696, 704-709, 1157-4245,4247-8375, 8387-8683, and 8686-9275.

According to an aspect of some embodiments of the present inventionthere is provided a nucleic acid construct comprising the isolatedpolynucleotide of some embodiments of the invention, and a promoter fordirecting transcription of the nucleic acid sequence in a host cell.

According to an aspect of some embodiments of the present inventionthere is provided an isolated polypeptide comprising an amino acidsequence at least 80% homologous to SEQ ID NO: 713-716, 718-734,737-741, 743-744, 746-765, 767-784, 786-788, 790-795, 797, 810-811,813-876, 878-889, 891-929, 931-1021, 1029-1064, 1067-1074, 1076-1080,1082-1088, 1091-1092, 1094-1153, 9283-9526, 9536, 9550-9772, 9825, 9832,9843-9881, 9899, 9908, 9925-9988, 9990-10284, 10290-11275, 11278-11279,11282-11284, 11289-11295, 11297-11299, 11301, 11303-11305, 11308-11312,11314, 11384, 11386, 11394, 11400, 11407, 11416-11417, 11421,11425-11426, 11429, 11433, 11439-11441, 11443-11444, 11446-11447,11449-11450, 11453-11455, 11457, 11460, 11468-11469, 11471, 11475,11482, 11485, 11488, 11494-11496, 11500-11503, 11505-11506, 11510-11513,11516-11525, 11530, 11551, 11555, 11559, 11561, 11570-11571, 11582,11589, 11605, 11612, 11695, 11697, 11699-13027, 13057, 13066,13091-13092, 13104, 13109, 13116, 13119-13180, 13188, 13192-13327,13329-13352, 13355-13929, 13941-13942, 13946-14913, 14989-15034,15037-15049, 15051-15072, 15074-15221, 15229-15252, 15254-15272,15281-15409, 15425, 15428-15434, 15455-15721 or 15722, wherein the aminoacid sequence is capable of increasing yield, growth rate, biomass,vigor, oil content, seed yield, fiber yield, fiber quality, fiberlength, photosynthetic capacity, nitrogen use efficiency, and/or abioticstress tolerance of a plant.

According to an aspect of some embodiments of the present inventionthere is provided an isolated polypeptide comprising the amino acidsequence selected from the group consisting of SEQ ID NOs: 713-735,737-741, 743-765, 767-795, 797, 809-1021, 1029-1064, 1067-1080,1082-1092, 1094-1153, 9276-9281, 9283-9532, 9534-9541, 9543-9545,9548-9774, 9776, 9778-9785, 9788-9791, 9793-9801, 9803, 9806-9807,9809-9820, 9822-9823, 9825-9838, 9840-9841, 9843-9881, 9889-9890,9893-9894, 9897-9899, 9901, 9904, 9906, 9908-9910, 9912-10285,10287-11276, 11278-11319, 11321, 11323, 11328-11330, 11333-11336,11339-11342, 11344-11355, 11357, 11359-11362, 11364-11366, 11369-13113,13115-13944, 13946-14913, 14915, 14917-14918, 14920-14921, 14923-14924,14927-14933, 14937, 14939-14940, 14942, 14944-14949, 14951, 14953,14955-14958, 14960-14962, 14964-14971, 14973, 14976, 14978-14979,14989-15221, 15225-15272, 15275-15410, 15412-15420, 15422-15423,15425-15426, 15428-15434, 15436, 15440-15441, 15443-15444, 15446,15448-15449, and 15451-15726.

According to an aspect of some embodiments of the present inventionthere is provided a plant cell exogenously expressing the polynucleotideof some embodiments of the invention, or the nucleic acid construct ofsome embodiments of the invention.

According to an aspect of some embodiments of the present inventionthere is provided a plant cell exogenously expressing the polypeptide ofsome embodiments of the invention.

According to some embodiments of the invention, the nucleic acidsequence encodes an amino acid sequence selected from the groupconsisting of SEQ ID NOs: 713-735, 737-741, 743-765, 767-795, 797,809-1021, 1029-1064, 1067-1080, 1082-1092, 1094-1153, 9276-9281,9283-9532, 9534-9541, 9543-9545, 9548-9774, 9776, 9778-9785, 9788-9791,9793-9801, 9803, 9806-9807, 9809-9820, 9822-9823, 9825-9838, 9840-9841,9843-9881, 9889-9890, 9893-9894, 9897-9899, 9901, 9904, 9906, 9908-9910,9912-10285, 10287-11276, 11278-11319, 11321, 11323, 11328-11330,11333-11336, 11339-11342, 11344-11355, 11357, 11359-11362, 11364-11366,11369-13113, 13115-13944, 13946-14913, 14915, 14917-14918, 14920-14921,14923-14924, 14927-14933, 14937, 14939-14940, 14942, 14944-14949, 14951,14953, 14955-14958, 14960-14962, 14964-14971, 14973, 14976, 14978-14979,14989-15221, 15225-15272, 15275-15410, 15412-15420, 15422-15423,15425-15426, 15428-15434, 15436, 15440-15441, 15443-15444, 15446,15448-15449, and 15451-15726.

According to some embodiments of the invention, the nucleic acidsequence is selected from the group consisting of SEQ ID NOs: 4-86, 88,100-312, 320-389, 391, 395-475, 477, 489-696, 704-709, 1157-4245,4247-8375, 8387-8683, and 8686-9275.

According to some embodiments of the invention, the polynucleotideconsists of the nucleic acid sequence selected from the group consistingof SEQ ID NOs: 4-86, 88, 100-312, 320-389, 391, 395-475, 477, 489-696,704-709, 1157-4245, 4247-8375, 8387-8683, and 8686-9275.

According to some embodiments of the invention, the nucleic acidsequence encodes the amino acid sequence selected from the groupconsisting of SEQ ID NOs: 713-735, 737-741, 743-765, 767-795, 797,809-1021, 1029-1064, 1067-1080, 1082-1092, 1094-1153, 9276-9281,9283-9532, 9534-9541, 9543-9545, 9548-9774, 9776, 9778-9785, 9788-9791,9793-9801, 9803, 9806-9807, 9809-9820, 9822-9823, 9825-9838, 9840-9841,9843-9881, 9889-9890, 9893-9894, 9897-9899, 9901, 9904, 9906, 9908-9910,9912-10285, 10287-11276, 11278-11319, 11321, 11323, 11328-11330,11333-11336, 11339-11342, 11344-11355, 11357, 11359-11362, 11364-11366,11369-13113, 13115-13944, 13946-14913, 14915, 14917-14918, 14920-14921,14923-14924, 14927-14933, 14937, 14939-14940, 14942, 14944-14949, 14951,14953, 14955-14958, 14960-14962, 14964-14971, 14973, 14976, 14978-14979,14989-15221, 15225-15272, 15275-15410, 15412-15420, 15422-15423,15425-15426, 15428-15434, 15436, 15440-15441, 15443-15444, 15446,15448-15449, and 15451-15726.

According to some embodiments of the invention, the plant cell formspart of a plant.

According to some embodiments of the invention, the method furthercomprising growing the plant expressing the exogenous polynucleotideunder the abiotic stress.

According to some embodiments of the invention, the abiotic stress isselected from the group consisting of salinity, drought, osmotic stress,water deprivation, flood, etiolation, low temperature, high temperature,heavy metal toxicity, anaerobiosis, nutrient deficiency, nitrogendeficiency, nutrient excess, atmospheric pollution and UV irradiation.

According to some embodiments of the invention, the yield comprises seedyield or oil yield.

According to an aspect of some embodiments of the present inventionthere is provided a transgenic plant comprising the nucleic acidconstruct of some embodiments of the invention or the plant cell of someembodiments of the invention.

According to some embodiments of the invention, the method furthercomprising growing the plant expressing the exogenous polynucleotideunder nitrogen-limiting conditions.

According to some embodiments of the invention, the promoter isheterologous to the isolated polynucleotide and/or to the host cell.

According to an aspect of some embodiments of the present inventionthere is provided a method of growing a crop, the method comprisingseeding seeds and/or planting plantlets of a plant transformed with theisolated polynucleotide of some embodiments of the invention, or withthe nucleic acid construct of some embodiments of the invention, whereinthe plant is derived from plants which have been transformed with theexogenous polynucleotide and which have been selected for at least onetrait selected from the group consisting of: increased nitrogen useefficiency, increased abiotic stress tolerance, increased biomass,increased growth rate, increased vigor, increased yield, increased fiberyield, increased fiber quality, increased fiber length, increasedphotosynthetic capacity, and increased oil content as compared to anon-transformed plant, thereby growing the crop.

According to some embodiments of the invention, the non-transformedplant is a wild type plant of identical genetic background.

According to some embodiments of the invention, the non-transformedplant is a wild type plant of the same species.

According to some embodiments of the invention, the non-transformedplant is grown under identical growth conditions.

According to some embodiments of the invention, the method furthercomprising selecting a plant having an increased yield, growth rate,biomass, vigor, oil content, seed yield, fiber yield, fiber quality,fiber length, photosynthetic capacity, nitrogen use efficiency, and/orabiotic stress tolerance as compared to the wild type plant of the samespecies which is grown under the same growth conditions.

According to an aspect of some embodiments of the present inventionthere is provided a method of selecting a transformed plant havingincreased yield, growth rate, biomass, vigor, oil content, seed yield,fiber yield, fiber quality, fiber length, photosynthetic capacity,nitrogen use efficiency, and/or abiotic stress tolerance as compared toa wild type plant of the same species which is grown under the samegrowth conditions, the method comprising:

(a) providing plants transformed with an exogenous polynucleotideencoding a polypeptide comprising an amino acid sequence at least 80%homologous to the amino acid sequence selected from the group consistingof SEQ ID NOs: 713-716, 718-734, 737-741, 743-744, 746-765, 767-784,786-788, 790-795, 797, 810-811, 813-876, 878-889, 891-929, 931-1021,1029-1064, 1067-1074, 1076-1080, 1082-1088, 1091-1092, 1094-1153,9283-9526, 9536, 9550-9772, 9825, 9832, 9843-9881, 9899, 9908,9925-9988, 9990-10284, 10290-11275, 11278-11279, 11282-11284,11289-11295, 11297-11299, 11301, 11303-11305, 11308-11312, 11314, 11384,11386, 11394, 11400, 11407, 11416-11417, 11421, 11425-11426, 11429,11433, 11439-11441, 11443-11444, 11446-11447, 11449-11450, 11453-11455,11457, 11460, 11468-11469, 11471, 11475, 11482, 11485, 11488,11494-11496, 11500-11503, 11505-11506, 11510-11513, 11516-11525, 11530,11551, 11555, 11559, 11561, 11570-11571, 11582, 11589, 11605, 11612,11695, 11697, 11699-13027, 13057, 13066, 13091-13092, 13104, 13109,13116, 13119-13180, 13188, 13192-13327, 13329-13352, 13355-13929,13941-13942, 13946-14913, 14989-15034, 15037-15049, 15051-15072,15074-15221, 15229-15252, 15254-15272, 15281-15409, 15425, 15428-15434,and 15455-15722,

(b) selecting from the plants of step (a) a plant having increasedyield, growth rate, biomass, vigor, oil content, seed yield, fiberyield, fiber quality, fiber length, photosynthetic capacity, nitrogenuse efficiency, and/or abiotic stress tolerance as compared to a wildtype plant of the same species which is grown under the same growthconditions, thereby selecting the plant having the increased yield,growth rate, biomass, vigor, oil content, seed yield, fiber yield, fiberquality, fiber length, photosynthetic capacity, nitrogen use efficiency,and/or abiotic stress tolerance as compared to the wild type plant ofthe same species which is grown under the same growth conditions.

According to an aspect of some embodiments of the present inventionthere is provided a method of selecting a transformed plant havingincreased yield, growth rate, biomass, vigor, oil content, seed yield,fiber yield, fiber quality, fiber length, photosynthetic capacity,nitrogen use efficiency, and/or abiotic stress tolerance as compared toa wild type plant of the same species which is grown under the samegrowth conditions, the method comprising:

(a) providing plants transformed with an exogenous polynucleotide atleast 80% identical to the nucleic acid sequence selected from the groupconsisting of SEQ ID NOs: 4-7, 9-25, 28-32, 34-35, 37-56, 58-75, 77-79,81-86, 88, 101-102, 104-167, 169-180, 182-220, 222-312, 320-389, 391,395-398, 400-416, 419-423, 425-426, 428-447, 449-464, 466-468, 470-475,477, 490-491, 493-555, 557-568, 570-605, 607-696, 704-709, 1164-1439,1453, 1468-1733, 1788, 1795, 1806-1860, 1884, 1899, 1917-2324,2331-3501, 3504-3506, 3509-3511, 3518-3526, 3528-3530, 3532, 3534-3536,3540-3547, 3549, 3638, 3641-3643, 3652, 3661, 3663, 3668, 3671,3683-3684, 3689, 3695-3696, 3700-3702, 3708, 3715-3718, 3720-3721,3723-3724, 3726-3727, 3732-3733, 3735, 3737, 3740, 3750-3751, 3753,3757, 3764-3765, 3768, 3772, 3776, 3783-3785, 3789-3792, 3794-3795,3800-3803, 3806-3818, 3827, 3889, 3894, 3898, 3900, 3915-3916, 3936,3943, 3964, 3971, 4099, 4101, 4103-4245, 4247-6064, 6103, 6112,6137-6138, 6150, 6155, 6162, 6165-6237, 6245, 6249-6406, 6408-6434,6437-7124, 7140-7141, 7145-8305, 8387-8453, 8457-8472, 8474-8505,8507-8683, 8691-8720, 8722-8748, 8757-8898, 8915, 8918-8927, and8948-9271,

(b) selecting from the plants of step (a) a plant having increasedyield, growth rate, biomass, vigor, oil content, seed yield, fiberyield, fiber quality, fiber length, photosynthetic capacity, nitrogenuse efficiency, and/or abiotic stress tolerance as compared to a wildtype plant of the same species which is grown under the same growthconditions, thereby selecting the plant having the increased yield,growth rate, biomass, vigor, oil content, seed yield, fiber yield, fiberquality, fiber length, photosynthetic capacity, nitrogen use efficiency,and/or abiotic stress tolerance as compared to the wild type plant ofthe same species which is grown under the same growth conditions.

According to an aspect of some embodiments of the present inventionthere is provided a method of growing a crop comprising:

(a) selecting a parent plant transformed with an exogenouspolynucleotide comprising a nucleic acid sequence encoding a polypeptideat least 80% homologous (e.g., identical) to the polypeptide selectedfrom the group consisting of set forth in SEQ ID NOs: 713-716, 718-734,737-741, 743-744, 746-765, 767-784, 786-788, 790-795, 797, 810-811,813-876, 878-889, 891-929, 931-1021, 1029-1064, 1067-1074, 1076-1080,1082-1088, 1091-1092, 1094-1153, 9283-9526, 9536, 9550-9772, 9825, 9832,9843-9881, 9899, 9908, 9925-9988, 9990-10284, 10290-11275, 11278-11279,11282-11284, 11289-11295, 11297-11299, 11301, 11303-11305, 11308-11312,11314, 11384, 11386, 11394, 11400, 11407, 11416-11417, 11421,11425-11426, 11429, 11433, 11439-11441, 11443-11444, 11446-11447,11449-11450, 11453-11455, 11457, 11460, 11468-11469, 11471, 11475,11482, 11485, 11488, 11494-11496, 11500-11503, 11505-11506, 11510-11513,11516-11525, 11530, 11551, 11555, 11559, 11561, 11570-11571, 11582,11589, 11605, 11612, 11695, 11697, 11699-13027, 13057, 13066,13091-13092, 13104, 13109, 13116, 13119-13180, 13188, 13192-13327,13329-13352, 13355-13929, 13941-13942, 13946-14913, 14989-15034,15037-15049, 15051-15072, 15074-15221, 15229-15252, 15254-15272,15281-15409, 15425, 15428-15434, and 15455-15722 for at least one traitselected from the group consisting of: increased yield, increased growthrate, increased biomass, increased vigor, increased oil content,increased seed yield, increased fiber yield, increased fiber quality,increased fiber length, increased photosynthetic capacity, increasednitrogen use efficiency, and increased abiotic stress tolerance ascompared to a non-transformed plant of the same species which is grownunder the same growth conditions, and

(b) growing progeny crop plant of said parent plant, wherein saidprogeny crop plant which comprises said exogenous polynucleotide hassaid increased yield, said increased growth rate, said increasedbiomass, said increased vigor, said increased oil content, saidincreased seed yield, said increased fiber yield, said increased fiberquality, said increased fiber length, said increased photosyntheticcapacity, said increased nitrogen use efficiency, and/or said increasedabiotic stress, thereby growing the crop.

According to an aspect of some embodiments of the present inventionthere is provided a method of producing seeds of a crop comprising:

(a) selecting parent plant transformed with an exogenous polynucleotidecomprising a nucleic acid sequence encoding a polypeptide at least 80%homologous (e.g., identical) to the polypeptide selected from the groupconsisting of set forth in SEQ ID NOs: 713-716, 718-734, 737-741,743-744, 746-765, 767-784, 786-788, 790-795, 797, 810-811, 813-876,878-889, 891-929, 931-1021, 1029-1064, 1067-1074, 1076-1080, 1082-1088,1091-1092, 1094-1153, 9283-9526, 9536, 9550-9772, 9825, 9832, 9843-9881,9899, 9908, 9925-9988, 9990-10284, 10290-11275, 11278-11279,11282-11284, 11289-11295, 11297-11299, 11301, 11303-11305, 11308-11312,11314, 11384, 11386, 11394, 11400, 11407, 11416-11417, 11421,11425-11426, 11429, 11433, 11439-11441, 11443-11444, 11446-11447,11449-11450, 11453-11455, 11457, 11460, 11468-11469, 11471, 11475,11482, 11485, 11488, 11494-11496, 11500-11503, 11505-11506, 11510-11513,11516-11525, 11530, 11551, 11555, 11559, 11561, 11570-11571, 11582,11589, 11605, 11612, 11695, 11697, 11699-13027, 13057, 13066,13091-13092, 13104, 13109, 13116, 13119-13180, 13188, 13192-13327,13329-13352, 13355-13929, 13941-13942, 13946-14913, 14989-15034,15037-15049, 15051-15072, 15074-15221, 15229-15252, 15254-15272,15281-15409, 15425, 15428-15434, and 15455-15722 for at least one traitselected from the group consisting of: increased yield, increased growthrate, increased biomass, increased vigor, increased oil content,increased seed yield, increased fiber yield, increased fiber quality,increased fiber length, increased photosynthetic capacity, increasednitrogen use efficiency, and increased abiotic stress as compared to anon-transformed plant of the same species which is grown under the samegrowth conditions,

(b) growing a seed producing plant from said parent plant resultant ofstep (a), wherein said seed producing plant which comprises saidexogenous polynucleotide having said increased yield, said increasedgrowth rate, said increased biomass, said increased vigor, saidincreased oil content, said increased seed yield, said increased fiberyield, said increased fiber quality, said increased fiber length, saidincreased photosynthetic capacity, said increased nitrogen useefficiency, and/or said increased abiotic stress, and

(c) producing seeds from said seed producing plant resultant of step(b), thereby producing seeds of the crop.

According to some embodiments of the invention, selecting is performedunder non-stress conditions.

According to some embodiments of the invention, selecting is performedunder abiotic stress conditions.

Unless otherwise defined, all technical and/or scientific terms usedherein have the same meaning as commonly understood by one of ordinaryskill in the art to which the invention pertains. Although methods andmaterials similar or equivalent to those described herein can be used inthe practice or testing of embodiments of the invention, exemplarymethods and/or materials are described below. In case of conflict, thepatent specification, including definitions, will control. In addition,the materials, methods, and examples are illustrative only and are notintended to be necessarily limiting.

BRIEF DESCRIPTION OF THE DRAWINGS

Some embodiments of the invention are herein described, by way ofexample only, with reference to the accompanying drawings. With specificreference now to the drawings in detail, it is stressed that theparticulars shown are by way of example and for purposes of illustrativediscussion of embodiments of the invention. In this regard, thedescription taken with the drawings makes apparent to those skilled inthe art how embodiments of the invention may be practiced.

In the drawings:

FIG. 1 is a schematic illustration of the modified pGI binary plasmidcontaining the new At6669 promoter (SEQ ID NO: 15751) and the GUSintron(pQYN 6669) used for expressing the isolated polynucleotide sequences ofthe invention. RB—T-DNA right border; LB—T-DNA left border; MCS—Multiplecloning site; RE—any restriction enzyme; NOS pro=nopaline synthasepromoter; NPT-II=neomycin phosphotransferase gene; NOS ter=nopalinesynthase terminator; Poly-A signal (polyadenylation signal);GUSintron—the GUS reporter gene (coding sequence and intron). Theisolated polynucleotide sequences of the invention were cloned into thevector while replacing the GUSintron reporter gene.

FIG. 2 is a schematic illustration of the modified pGI binary plasmidcontaining the new At6669 promoter (SEQ ID NO: 15751) (pQFN or pQFNc)used for expressing the isolated polynucleotide sequences of theinvention. RB—T-DNA right border; LB—T-DNA left border; MCS—Multiplecloning site; RE—any restriction enzyme; NOS pro=nopaline synthasepromoter; NPT-II=neomycin phosphotransferase gene; NOS ter=nopalinesynthase terminator; Poly-A signal (polyadenylation signal); Theisolated polynucleotide sequences of the invention were cloned into theMCS of the vector.

FIGS. 3A-F are images depicting visualization of root development oftransgenic plants exogenously expressing the polynucleotide of someembodiments of the invention when grown in transparent agar plates undernormal (FIGS. 3A-B), osmotic stress (15% PEG; FIGS. 3C-D) ornitrogen-limiting (FIGS. 3E-F) conditions. The different transgenes weregrown in transparent agar plates for 17 days (7 days nursery and 10 daysafter transplanting). The plates were photographed every 3-4 daysstarting at day 1 after transplanting. FIG. 3A—An image of a photographof plants taken following 10 after transplanting days on agar plateswhen grown under normal (standard) conditions. FIG. 3B—An image of rootanalysis of the plants shown in FIG. 3A in which the lengths of theroots measured are represented by arrows. FIG. 3C—An image of aphotograph of plants taken following 10 days after transplanting on agarplates, grown under high osmotic (PEG 15%) conditions. FIG. 3D—An imageof root analysis of the plants shown in FIG. 3C in which the lengths ofthe roots measured are represented by arrows. FIG. 3E—An image of aphotograph of plants taken following 10 days after transplanting on agarplates, grown under low nitrogen conditions. FIG. 3F—An image of rootanalysis of the plants shown in FIG. 3E in which the lengths of theroots measured are represented by arrows.

FIG. 4 is a schematic illustration of the modified pGI binary plasmidcontaining the Root Promoter (pQNa RP) used for expressing the isolatedpolynucleotide sequences of the invention. RB—T-DNA right border;LB—T-DNA left border; NOS pro=nopaline synthase promoter;NPT-II=neomycin phosphotransferase gene; NOS ter=nopaline synthaseterminator; Poly-A signal (polyadenylation signal); The isolatedpolynucleotide sequences according to some embodiments of the inventionwere cloned into the MCS (Multiple cloning site) of the vector.

FIG. 5 is a schematic illustration of the pQYN plasmid.

FIG. 6 is a schematic illustration of the pQFN plasmid.

FIG. 7 is a schematic illustration of the pQFYN plasmid.

FIG. 8 is a schematic illustration of the modified pGI binary plasmid(pQXNc) used for expressing the isolated polynucleotide sequences ofsome embodiments of the invention. RB—T-DNA right border; LB—T-DNA leftborder; NOS pro=nopaline synthase promoter; NPT-II=neomycinphosphotransferase gene; NOS ter=nopaline synthase terminator; RE=anyrestriction enzyme; Poly-A signal (polyadenylation signal); 35S—the 35Spromoter (pqfnc; SEQ ID NO: 15747). The isolated polynucleotidesequences of some embodiments of the invention were cloned into the MCS(Multiple cloning site) of the vector.

FIGS. 9A-B are schematic illustrations of the pEBbVNi tDNA (FIG. 9A) andthe pEBbNi tDNA (FIG. 9B) plasmids used in the Brachypodium experiments.pEBbVNi tDNA (FIG. 9A) was used for expression of the isolatedpolynucleotide sequences of some embodiments of the invention inBrachypodium. pEBbNi tDNA (FIG. 9B) was used for transformation intoBrachypodium as a negative control. “RB”=right border; “2LBregion”=2repeats of left border; “35S”=35S promoter (SEQ ID NO: 15763); “NOSter”=nopaline synthase terminator; “Bar ORF”—BAR open reading frame(GenBank Accession No. JQ293091.1; SEQ ID NO: 15764); The isolatedpolynucleotide sequences of some embodiments of the invention werecloned into the Multiple cloning site of the vector using one or more ofthe indicated restriction enzyme sites.

FIG. 10 depicts seedling analysis of an Arabidopsis plant having shoots(upper part, marked “#1”) and roots (lower part, marked “#2”). Using animage analysis system the minimal convex area encompassed by the rootsis determined. Such area corresponds to the root coverage of the plant.

DESCRIPTION OF SPECIFIC EMBODIMENTS OF THE INVENTION

The present invention, in some embodiments thereof, relates to isolatedpolynucleotides and polypeptides, nucleic acid constructs, transgeniccells and transgenic plants comprising same and methods of generatingand using same, and, more particularly, but not exclusively, to methodsof increasing yield, biomass, growth rate, vigor, oil content, fiberyield, fiber quality abiotic stress tolerance, and/or fertilizer useefficiency (e.g., nitrogen use efficiency) of a plant.

Before explaining at least one embodiment of the invention in detail, itis to be understood that the invention is not necessarily limited in itsapplication to the details set forth in the following description orexemplified by the Examples. The invention is capable of otherembodiments or of being practiced or carried out in various ways.

The present inventors have identified novel polypeptides andpolynucleotides which can be used to generate nucleic acid constructs,transgenic plants and to increase nitrogen use efficiency, fertilizeruse efficiency, yield, growth rate, vigor, biomass, oil content, fiberyield, fiber quality, fiber length, photosynthetic capacity, abioticstress tolerance and/or water use efficiency of a plant, such as a wheatplant.

Thus, as shown in the Examples section which follows, the presentinventors have utilized bioinformatics tools to identify polynucleotideswhich enhance/increase fertilizer use efficiency (e.g., nitrogen useefficiency), yield (e.g., seed yield, oil yield, oil content), growthrate, biomass, vigor, fiber yield, fiber quality, fiber length,photosynthetic capacity, and/or abiotic stress tolerance of a plant.Genes which affect the trait-of-interest were identified (SEQ ID NOs:710-1153 for polypeptides; and SEQ ID NOs: 1-709 for polypeptides) basedon expression profiles of genes of several Arabidopsis, Barley, Sorghum,Maize, tomato, and Foxtail millet ecotypes and accessions in varioustissues and growth conditions, homology with genes known to affect thetrait-of-interest and using digital expression profile in specifictissues and conditions (Tables 1, 3-171, Examples 1 and 3-21 of theExamples section which follows). Homologous (e.g., orthologous)polypeptides and polynucleotides having the same function were alsoidentified [SEQ ID NOs: 9276-15726 (for polypeptides), and SEQ ID NOs:1157-9275 (for polynucleotides); Table 2, Example 2 of the Examplessection which follows]. The polynucleotides of some embodiments of theinvention were cloned into binary vectors (Example 22, Table 172), andwere further transformed into Arabidopsis and Brachypodium plants(Examples 23-25). Transgenic plants over-expressing the identifiedpolynucleotides were found to exhibit increased biomass, growth rate,vigor, photosynthetic capacity (e.g., increased leaf area forphotosynthesis) and yield under normal growth conditions or undernitrogen limiting growth conditions (Tables 173-187; Examples 26-28),and increased tolerance to abiotic stress conditions (e.g., nutrientdeficiency) as compared to control plants grown under the same growthconditions. Altogether, these results suggest the use of the novelpolynucleotides and polypeptides of the invention [e.g., SEQ ID NOs:713-735, 737-741, 743-765, 767-795, 797, 809-1021, 1029-1064, 1067-1080,1082-1092, 1094-1153, 9276-9281, 9283-9532, 9534-9541, 9543-9545,9548-9774, 9776, 9778-9785, 9788-9791, 9793-9801, 9803, 9806-9807,9809-9820, 9822-9823, 9825-9838, 9840-9841, 9843-9881, 9889-9890,9893-9894, 9897-9899, 9901, 9904, 9906, 9908-9910, 9912-10285,10287-11276, 11278-11319, 11321, 11323, 11328-11330, 11333-11336,11339-11342, 11344-11355, 11357, 11359-11362, 11364-11366, 11369-13113,13115-13944, 13946-14913, 14915, 14917-14918, 14920-14921, 14923-14924,14927-14933, 14937, 14939-14940, 14942, 14944-14949, 14951, 14953,14955-14958, 14960-14962, 14964-14971, 14973, 14976, 14978-14979,14989-15221, 15225-15272, 15275-15410, 15412-15420, 15422-15423,15425-15426, 15428-15434, 15436, 15440-15441, 15443-15444, 15446,15448-15449, and 15451-15726 (polypeptides) and SEQ ID NOs: 4-86, 88,100-312, 320-389, 391, 395-475, 477, 489-696, 704-709, 1157-4245,4247-8375, 8387-8683, and 8686-9275 (polynucleotides)] for increasingnitrogen use efficiency, fertilizer use efficiency, yield (e.g., oilyield, seed yield and oil content), growth rate, biomass, vigor, fiberyield, fiber quality, fiber length, photosynthetic capacity, water useefficiency and/or abiotic stress tolerance of a plant.

Thus, according to an aspect of some embodiments of the invention, thereis provided method of increasing yield, growth rate, biomass, vigor, oilcontent, fiber yield, fiber quality, fiber length, photosyntheticcapacity, fertilizer use efficiency (e.g., nitrogen use efficiency)and/or abiotic stress tolerance of a plant, comprising expressing withinthe plant an exogenous polynucleotide comprising a nucleic acid sequenceencoding a polypeptide at least about 80%, at least about 81%, at leastabout 82%, at least about 83%, at least about 84%, at least about 85%,at least about 86%, at least about 87%, at least about 88%, at leastabout 89%, at least about 90%, at least about 91%, at least about 92%,at least about 93%, at least about 94%, at least about 95%, at leastabout 96%, at least about 97%, at least about 98%, at least about 99%,or more say 100% homologous to the amino acid sequence selected from thegroup consisting of SEQ ID NOs: 713-716, 718-734, 737-741, 743-744,746-765, 767-784, 786-788, 790-795, 797, 810-811, 813-876, 878-889,891-929, 931-1021, 1029-1064, 1067-1074, 1076-1080, 1082-1088,1091-1092, 1094-1153, 9283-9526, 9536, 9550-9772, 9825, 9832, 9843-9881,9899, 9908, 9925-9988, 9990-10284, 10290-11275, 11278-11279,11282-11284, 11289-11295, 11297-11299, 11301, 11303-11305, 11308-11312,11314, 11384, 11386, 11394, 11400, 11407, 11416-11417, 11421,11425-11426, 11429, 11433, 11439-11441, 11443-11444, 11446-11447,11449-11450, 11453-11455, 11457, 11460, 11468-11469, 11471, 11475,11482, 11485, 11488, 11494-11496, 11500-11503, 11505-11506, 11510-11513,11516-11525, 11530, 11551, 11555, 11559, 11561, 11570-11571, 11582,11589, 11605, 11612, 11695, 11697, 11699-13027, 13057, 13066,13091-13092, 13104, 13109, 13116, 13119-13180, 13188, 13192-13327,13329-13352, 13355-13929, 13941-13942, 13946-14913, 14989-15034,15037-15049, 15051-15072, 15074-15221, 15229-15252, 15254-15272,15281-15409, 15425, 15428-15434, and 15455-15722, thereby increasing theyield, growth rate, biomass, vigor, oil content, fiber yield, fiberquality, fiber length, photosynthetic capacity, fertilizer useefficiency (e.g., nitrogen use efficiency) and/or abiotic stresstolerance of the plant.

As used herein the phrase “plant yield” refers to the amount (e.g., asdetermined by weight or size) or quantity (numbers) of tissues or organsproduced per plant or per growing season. Hence increased yield couldaffect the economic benefit one can obtain from the plant in a certaingrowing area and/or growing time.

It should be noted that a plant yield can be affected by variousparameters including, but not limited to, plant biomass; plant vigor;growth rate; seed yield; seed or grain quantity; seed or grain quality;oil yield; content of oil, starch and/or protein in harvested organs(e.g., seeds or vegetative parts of the plant); number of flowers(florets) per panicle (expressed as a ratio of number of filled seedsover number of primary panicles); harvest index; number of plants grownper area; number and size of harvested organs per plant and per area;number of plants per growing area (density); number of harvested organsin field; total leaf area; carbon assimilation and carbon partitioning(the distribution/allocation of carbon within the plant); resistance toshade; number of harvestable organs (e.g. seeds), seeds per pod, weightper seed; and modified architecture [such as increase stalk diameter,thickness or improvement of physical properties (e.g. elasticity)].

As used herein the phrase “seed yield” refers to the number or weight ofthe seeds per plant, seeds per pod, or per growing area or to the weightof a single seed, or to the oil extracted per seed. Hence seed yield canbe affected by seed dimensions (e.g., length, width, perimeter, areaand/or volume), number of (filled) seeds and seed filling rate and byseed oil content. Hence increase seed yield per plant could affect theeconomic benefit one can obtain from the plant in a certain growing areaand/or growing time; and increase seed yield per growing area could beachieved by increasing seed yield per plant, and/or by increasing numberof plants grown on the same given area.

The term “seed” (also referred to as “grain” or “kernel”) as used hereinrefers to a small embryonic plant enclosed in a covering called the seedcoat (usually with some stored food), the product of the ripened ovuleof gymnosperm and angiosperm plants which occurs after fertilization andsome growth within the mother plant.

The phrase “oil content” as used herein refers to the amount of lipidsin a given plant organ, either the seeds (seed oil content) or thevegetative portion of the plant (vegetative oil content) and istypically expressed as percentage of dry weight (10% humidity of seeds)or wet weight (for vegetative portion).

It should be noted that oil content is affected by intrinsic oilproduction of a tissue (e.g., seed, vegetative portion), as well as themass or size of the oil-producing tissue per plant or per growth period.

In one embodiment, increase in oil content of the plant can be achievedby increasing the size/mass of a plant's tissue(s) which comprise oilper growth period. Thus, increased oil content of a plant can beachieved by increasing the yield, growth rate, biomass and vigor of theplant.

As used herein the phrase “plant biomass” refers to the amount (e.g.,measured in grams of air-dry tissue) of a tissue produced from the plantin a growing season, which could also determine or affect the plantyield or the yield per growing area. An increase in plant biomass can bein the whole plant or in parts thereof such as aboveground (harvestable)parts, vegetative biomass, roots and seeds.

As used herein the term “root biomass” refers to the total weight of theplant's root(s). Root biomass can be determined directly by weighing thetotal root material (fresh and/or dry weight) of a plant.

Additional or alternatively, the root biomass can be indirectlydetermined by measuring root coverage, root density and/or root lengthof a plant.

It should be noted that plants having a larger root coverage exhibithigher fertilizer (e.g., nitrogen) use efficiency and/or higher wateruse efficiency as compared to plants with a smaller root coverage.

As used herein the phrase “root coverage” refers to the total area orvolume of soil or of any plant-growing medium encompassed by the rootsof a plant.

According to some embodiments of the invention, the root coverage is theminimal convex volume encompassed by the roots of the plant.

It should be noted that since each plant has a characteristic rootsystem, e.g., some plants exhibit a shallow root system (e.g., only afew centimeters below ground level), while others have a deep in soilroot system (e.g., a few tens of centimeters or a few meters deep insoil below ground level), measuring the root coverage of a plant can beperformed in any depth of the soil or of the plant-growing medium, andcomparison of root coverage between plants of the same species (e.g., atransgenic plant exogenously expressing the polynucleotide of someembodiments of the invention and a control plant) should be performed bymeasuring the root coverage in the same depth.

According to some embodiments of the invention, the root coverage is theminimal convex area encompassed by the roots of a plant in a specificdepth.

A non-limiting example of measuring root coverage is shown in FIG. 10.

As used herein the term “root density” refers to the density of roots ina given area (e.g., area of soil or any plant growing medium). The rootdensity can be determined by counting the root number per apredetermined area at a predetermined depth (in units of root number perarea, e.g., mm², cm² or m²).

As used herein the phrase “root length” refers to the total length ofthe longest root of a single plant.

As used herein the phrase “root length growth rate” refers to the changein total root length per plant per time unit (e.g., per day).

As used herein the phrase “growth rate” refers to the increase in plantorgan/tissue size per time (can be measured in cm² per day or cm/day).

As used herein the phrase “photosynthetic capacity” (also known as“A_(max)”) is a measure of the maximum rate at which leaves are able tofix carbon during photosynthesis. It is typically measured as the amountof carbon dioxide that is fixed per square meter per second, for exampleas μmol m⁻² sec⁻¹. Plants are able to increase their photosyntheticcapacity by several modes of action, such as by increasing the totalleaves area (e.g., by increase of leaves area, increase in the number ofleaves, and increase in plant's vigor, e.g., the ability of the plant togrow new leaves along time course) as well as by increasing the abilityof the plant to efficiently execute carbon fixation in the leaves.Hence, the increase in total leaves area can be used as a reliablemeasurement parameter for photosynthetic capacity increment.

As used herein the phrase “plant vigor” refers to the amount (measuredby weight) of tissue produced by the plant in a given time. Henceincreased vigor could determine or affect the plant yield or the yieldper growing time or growing area. In addition, early vigor (seed and/orseedling) results in improved field stand.

Improving early vigor is an important objective of modern rice breedingprograms in both temperate and tropical rice cultivars. Long roots areimportant for proper soil anchorage in water-seeded rice. Where rice issown directly into flooded fields, and where plants must emerge rapidlythrough water, longer shoots are associated with vigour. Wheredrill-seeding is practiced, longer mesocotyls and coleoptiles areimportant for good seedling emergence. The ability to engineer earlyvigor into plants would be of great importance in agriculture. Forexample, poor early vigor has been a limitation to the introduction ofmaize (Zea mays L.) hybrids based on Corn Belt germplasm in the EuropeanAtlantic.

It should be noted that a plant trait such as yield, growth rate,biomass, vigor, oil content, fiber yield, fiber quality, fiber length,photosynthetic capacity, fertilizer use efficiency (e.g., nitrogen useefficiency) can be determined under stress (e.g., abiotic stress,nitrogen-limiting conditions) and/or non-stress (normal) conditions.

As used herein, the phrase “non-stress conditions” refers to the growthconditions (e.g., water, temperature, light-dark cycles, humidity, saltconcentration, fertilizer concentration in soil, nutrient supply such asnitrogen, phosphorous and/or potassium), that do not significantly gobeyond the everyday climatic and other abiotic conditions that plantsmay encounter, and which allow optimal growth, metabolism, reproductionand/or viability of a plant at any stage in its life cycle (e.g., in acrop plant from seed to a mature plant and back to seed again). Personsskilled in the art are aware of normal soil conditions and climaticconditions for a given plant in a given geographic location. It shouldbe noted that while the non-stress conditions may include some mildvariations from the optimal conditions (which vary from one type/speciesof a plant to another), such variations do not cause the plant to ceasegrowing without the capacity to resume growth.

One unit of nitrogen refers to one kg (kilogram) of total nitrogen perdunam (1000 m²).

Following is a non-limiting description of non-stress (normal) growthconditions which can be used for growing the transgenic plantsexpressing the polynucleotides or polypeptides of some embodiments ofthe invention.

For example, normal conditions for growing sorghum include irrigationwith about 452,000 liter water per dunam (1000 square meters) andfertilization with about 14 units nitrogen per dunam per growing season.

Normal conditions for growing cotton include irrigation with about580,000 liter water per dunam (1000 square meters) and fertilizationwith about 24 units nitrogen per dunam per growing season.

Normal conditions for growing bean include irrigation with about 524,000liter water per dunam (1000 square meters) and fertilization with about16 units nitrogen per dunam per growing season.

Normal conditions for growing B. Juncea include irrigation with about861,000 liter water per dunam (1000 square meters) and fertilizationwith about 12 units nitrogen per dunam per growing season.

The phrase “abiotic stress” as used herein refers to any adverse effecton metabolism, growth, reproduction and/or viability of a plant.Accordingly, abiotic stress can be induced by suboptimal environmentalgrowth conditions such as, for example, salinity, osmotic stress, waterdeprivation, drought, flooding, freezing, low or high temperature, heavymetal toxicity, anaerobiosis, nutrient deficiency (e.g., nitrogendeficiency or limited nitrogen), atmospheric pollution or UVirradiation. The implications of abiotic stress are discussed in theBackground section.

The phrase “abiotic stress tolerance” as used herein refers to theability of a plant to endure an abiotic stress without suffering asubstantial alteration in metabolism, growth, productivity and/orviability.

Plants are subject to a range of environmental challenges. Several ofthese, including salt stress, general osmotic stress, drought stress andfreezing stress, have the ability to impact whole plant and cellularwater availability. Not surprisingly, then, plant responses to thiscollection of stresses are related. Zhu (2002) Ann Rev. Plant Biol. 53:247-273 et al. note that “most studies on water stress signaling havefocused on salt stress primarily because plant responses to salt anddrought are closely related and the mechanisms overlap”. Many examplesof similar responses and pathways to this set of stresses have beendocumented. For example, the CBF transcription factors have been shownto condition resistance to salt, freezing and drought (Kasuga et al.(1999) Nature Biotech. 17: 287-291). The Arabidopsis rd29B gene isinduced in response to both salt and dehydration stress, a process thatis mediated largely through an ABA signal transduction process (Uno etal. (2000) Proc. Natl. Acad. Sci. USA 97: 11632-11637), resulting inaltered activity of transcription factors that bind to an upstreamelement within the rd29B promoter. In Mesembryanthemum crystallinum (iceplant), Patharker and Cushman have shown that a calcium-dependentprotein kinase (McCDPK1) is induced by exposure to both drought and saltstresses (Patharker and Cushman (2000) Plant J. 24: 679-691). Thestress-induced kinase was also shown to phosphorylate a transcriptionfactor, presumably altering its activity, although transcript levels ofthe target transcription factor are not altered in response to salt ordrought stress. Similarly, Saijo et al. demonstrated that a ricesalt/drought-induced calmodulin-dependent protein kinase (OsCDPK7)conferred increased salt and drought tolerance to rice whenoverexpressed (Saijo et al. (2000) Plant J. 23: 319-327).

Exposure to dehydration invokes similar survival strategies in plants asdoes freezing stress (see, for example, Yelenosky (1989) Plant Physiol89: 444-451) and drought stress induces freezing tolerance (see, forexample, Siminovitch et al. (1982) Plant Physiol 69: 250-255; and Guy etal. (1992) Planta 188: 265-270). In addition to the induction ofcold-acclimation proteins, strategies that allow plants to survive inlow water conditions may include, for example, reduced surface area, orsurface oil or wax production. In another example increased solutecontent of the plant prevents evaporation and water loss due to heat,drought, salinity, osmoticum, and the like therefore providing a betterplant tolerance to the above stresses.

It will be appreciated that some pathways involved in resistance to onestress (as described above), will also be involved in resistance toother stresses, regulated by the same or homologous genes. Of course,the overall resistance pathways are related, not identical, andtherefore not all genes controlling resistance to one stress willcontrol resistance to the other stresses. Nonetheless, if a geneconditions resistance to one of these stresses, it would be apparent toone skilled in the art to test for resistance to these related stresses.Methods of assessing stress resistance are further provided in theExamples section which follows.

As used herein the phrase “water use efficiency (WUE)” refers to thelevel of organic matter produced per unit of water consumed by theplant, i.e., the dry weight of a plant in relation to the plant's wateruse, e.g., the biomass produced per unit transpiration.

As used herein the phrase “fertilizer use efficiency” refers to themetabolic process(es) which lead to an increase in the plant's yield,biomass, vigor, and growth rate per fertilizer unit applied. Themetabolic process can be the uptake, spread, absorbent, accumulation,relocation (within the plant) and use of one or more of the minerals andorganic moieties absorbed by the plant, such as nitrogen, phosphatesand/or potassium.

As used herein the phrase “fertilizer-limiting conditions” refers togrowth conditions which include a level (e.g., concentration) of afertilizer applied which is below the level needed for normal plantmetabolism, growth, reproduction and/or viability.

As used herein the phrase “nitrogen use efficiency (NUE)” refers to themetabolic process(es) which lead to an increase in the plant's yield,biomass, vigor, and growth rate per nitrogen unit applied. The metabolicprocess can be the uptake, spread, absorbent, accumulation, relocation(within the plant) and use of nitrogen absorbed by the plant.

As used herein the phrase “nitrogen-limiting conditions” refers togrowth conditions which include a level (e.g., concentration) ofnitrogen (e g, ammonium or nitrate) applied which is below the levelneeded for normal plant metabolism, growth, reproduction and/orviability.

Improved plant NUE and FUE is translated in the field into eitherharvesting similar quantities of yield, while implementing lessfertilizers, or increased yields gained by implementing the same levelsof fertilizers. Thus, improved NUE or FUE has a direct effect on plantyield in the field. Thus, the polynucleotides and polypeptides of someembodiments of the invention positively affect plant yield, seed yield,and plant biomass. In addition, the benefit of improved plant NUE willcertainly improve crop quality and biochemical constituents of the seedsuch as protein yield and oil yield. It should be noted that improvedABST will confer plants with improved vigor also under non-stressconditions, resulting in crops having improved biomass and/or yielde.g., elongated fibers for the cotton industry, higher oil content.

The term “fiber” is usually inclusive of thick-walled conducting cellssuch as vessels and tracheids and to fibrillar aggregates of manyindividual fiber cells. Hence, the term “fiber” refers to (a)thick-walled conducting and non-conducting cells of the xylem; (b)fibers of extraxylary origin, including those from phloem, bark, groundtissue, and epidermis; and (c) fibers from stems, leaves, roots, seeds,and flowers or inflorescences (such as those of Sorghum vulgare used inthe manufacture of brushes and brooms).

Example of fiber producing plants, include, but are not limited to,agricultural crops such as cotton, silk cotton tree (Kapok, Ceibapentandra), desert willow, creosote bush, winterfat, balsa, kenaf,roselle, jute, sisal abaca, flax, corn, sugar cane, hemp, ramie, kapok,coir, bamboo, spanish moss and Agave spp. (e.g. sisal).

As used herein the phrase “fiber quality” refers to at least one fiberparameter which is agriculturally desired, or required in the fiberindustry (further described hereinbelow). Examples of such parameters,include but are not limited to, fiber length, fiber strength, fiberfitness, fiber weight per unit length, maturity ratio and uniformity(further described hereinbelow).

Cotton fiber (lint) quality is typically measured according to fiberlength, strength and fineness. Accordingly, the lint quality isconsidered higher when the fiber is longer, stronger and finer.

As used herein the phrase “fiber yield” refers to the amount or quantityof fibers produced from the fiber producing plant.

As used herein the term “increasing” refers to at least about 2%, atleast about 3%, at least about 4%, at least about 5%, at least about10%, at least about 15%, at least about 20%, at least about 30%, atleast about 40%, at least about 50%, at least about 60%, at least about70%, at least about 80%, increase in yield, seed yield, biomass, growthrate, vigor, oil content, fiber yield, fiber quality, fiber length,photosynthetic capacity, abiotic stress tolerance, and/or nitrogen useefficiency of a plant as compared to a native plant or a wild type plant[i.e., a plant not modified with the biomolecules (polynucleotide orpolypeptides) of the invention, e.g., a non-transformed plant of thesame species which is grown under the same (e.g., identical) growthconditions].

The phrase “expressing within the plant an exogenous polynucleotide” asused herein refers to upregulating the expression level of an exogenouspolynucleotide within the plant by introducing the exogenouspolynucleotide into a plant cell or plant and expressing by recombinantmeans, as further described herein below.

As used herein “expressing” refers to expression at the mRNA andoptionally polypeptide level.

As used herein, the phrase “exogenous polynucleotide” refers to aheterologous nucleic acid sequence which may not be naturally expressedwithin the plant (e.g., a nucleic acid sequence from a differentspecies) or which overexpression in the plant is desired. The exogenouspolynucleotide may be introduced into the plant in a stable or transientmanner, so as to produce a ribonucleic acid (RNA) molecule and/or apolypeptide molecule. It should be noted that the exogenouspolynucleotide may comprise a nucleic acid sequence which is identicalor partially homologous to an endogenous nucleic acid sequence of theplant.

The term “endogenous” as used herein refers to any polynucleotide orpolypeptide which is present and/or naturally expressed within a plantor a cell thereof.

According to some embodiments of the invention, the exogenouspolynucleotide of the invention comprises a nucleic acid sequenceencoding a polypeptide having an amino acid sequence at least about 80%,at least about 81%, at least about 82%, at least about 83%, at leastabout 84%, at least about 85%, at least about 86%, at least about 87%,at least about 88%, at least about 89%, at least about 90%, at leastabout 91%, at least about 92%, at least about 93%, at least about 94%,at least about 95%, at least about 96%, at least about 97%, at leastabout 98%, at least about 99%, or more say 100% homologous (e.g.,identical) to the amino acid sequence selected from the group consistingof SEQ ID NOs: 713-716, 718-734, 737-741, 743-744, 746-765, 767-784,786-788, 790-795, 797, 810-811, 813-876, 878-889, 891-929, 931-1021,1029-1064, 1067-1074, 1076-1080, 1082-1088, 1091-1092, 1094-1153,9283-9526, 9536, 9550-9772, 9825, 9832, 9843-9881, 9899, 9908,9925-9988, 9990-10284, 10290-11275, 11278-11279, 11282-11284,11289-11295, 11297-11299, 11301, 11303-11305, 11308-11312, 11314, 11384,11386, 11394, 11400, 11407, 11416-11417, 11421, 11425-11426, 11429,11433, 11439-11441, 11443-11444, 11446-11447, 11449-11450, 11453-11455,11457, 11460, 11468-11469, 11471, 11475, 11482, 11485, 11488,11494-11496, 11500-11503, 11505-11506, 11510-11513, 11516-11525, 11530,11551, 11555, 11559, 11561, 11570-11571, 11582, 11589, 11605, 11612,11695, 11697, 11699-13027, 13057, 13066, 13091-13092, 13104, 13109,13116, 13119-13180, 13188, 13192-13327, 13329-13352, 13355-13929,13941-13942, 13946-14913, 14989-15034, 15037-15049, 15051-15072,15074-15221, 15229-15252, 15254-15272, 15281-15409, 15425, 15428-15434,and 15455-15722.

Homologous sequences include both orthologous and paralogous sequences.The term “paralogous” relates to gene-duplications within the genome ofa species leading to paralogous genes. The term “orthologous” relates tohomologous genes in different organisms due to ancestral relationship.Thus, orthologs are evolutionary counterparts derived from a singleancestral gene in the last common ancestor of given two species (KooninEV and Galperin MY (Sequence-Evolution-Function: ComputationalApproaches in Comparative Genomics. Boston: Kluwer Academic; 2003.Chapter 2, Evolutionary Concept in Genetics and Genomics. Availablefrom: ncbi (dot) nlm (dot) nih (dot) gov/books/NBK20255) and thereforehave great likelihood of having the same function.

One option to identify orthologues in monocot plant species is byperforming a reciprocal blast search. This may be done by a first blastinvolving blasting the sequence-of-interest against any sequencedatabase, such as the publicly available NCBI database which may befound at: ncbi (dot) nlm (dot) nih (dot) gov. If orthologues in ricewere sought, the sequence-of-interest would be blasted against, forexample, the 28,469 full-length cDNA clones from Oryza sativa Nipponbareavailable at NCBI. The blast results may be filtered. The full-lengthsequences of either the filtered results or the non-filtered results arethen blasted back (second blast) against the sequences of the organismfrom which the sequence-of-interest is derived. The results of the firstand second blasts are then compared. An orthologue is identified whenthe sequence resulting in the highest score (best hit) in the firstblast identifies in the second blast the query sequence (the originalsequence-of-interest) as the best hit. Using the same rational aparalogue (homolog to a gene in the same organism) is found. In case oflarge sequence families, the ClustalW program may be used [ebi (dot) ac(dot) uk/Tools/clustalw2/index (dot) html], followed by aneighbor-joining tree (wikipedia (dot) org/wiki/Neighbor-joining) whichhelps visualizing the clustering.

Homology (e.g., percent homology, sequence identity+sequence similarity)can be determined using any homology comparison software computing apairwise sequence alignment.

As used herein, “sequence identity” or “identity” in the context of twonucleic acid or polypeptide sequences includes reference to the residuesin the two sequences which are the same when aligned. When percentage ofsequence identity is used in reference to proteins it is recognized thatresidue positions which are not identical often differ by conservativeamino acid substitutions, where amino acid residues are substituted forother amino acid residues with similar chemical properties (e.g. chargeor hydrophobicity) and therefore do not change the functional propertiesof the molecule. Where sequences differ in conservative substitutions,the percent sequence identity may be adjusted upwards to correct for theconservative nature of the substitution. Sequences which differ by suchconservative substitutions are considered to have “sequence similarity”or “similarity”. Means for making this adjustment are well-known tothose of skill in the art. Typically this involves scoring aconservative substitution as a partial rather than a full mismatch,thereby increasing the percentage sequence identity. Thus, for example,where an identical amino acid is given a score of 1 and anon-conservative substitution is given a score of zero, a conservativesubstitution is given a score between zero and 1. The scoring ofconservative substitutions is calculated, e.g., according to thealgorithm of Henikoff S and Henikoff J G. [Amino acid substitutionmatrices from protein blocks. Proc. Natl. Acad. Sci. U.S.A. 1992,89(22): 10915-9].

Identity (e.g., percent homology) can be determined using any homologycomparison software, including for example, the BlastN software of theNational Center of Biotechnology Information (NCBI) such as by usingdefault parameters.

According to some embodiments of the invention, the identity is a globalidentity, i.e., an identity over the entire amino acid or nucleic acidsequences of the invention and not over portions thereof.

According to some embodiments of the invention, the term “homology” or“homologous” refers to identity of two or more nucleic acid sequences;or identity of two or more amino acid sequences; or the identity of anamino acid sequence to one or more nucleic acid sequence.

According to some embodiments of the invention, the homology is a globalhomology, i.e., an homology over the entire amino acid or nucleic acidsequences of the invention and not over portions thereof.

The degree of homology or identity between two or more sequences can bedetermined using various known sequence comparison tools. Following is anon-limiting description of such tools which can be used along with someembodiments of the invention.

Pairwise global alignment was defined by S. B. Needleman and C. D.Wunsch, “A general method applicable to the search of similarities inthe amino acid sequence of two proteins” Journal of Molecular Biology,1970, pages 443-53, volume 48).

For example, when starting from a polypeptide sequence and comparing toother polypeptide sequences, the EMBOSS-6.0.1 Needleman-Wunsch algorithm(available fromemboss(dot)sourceforge(dot)net/apps/cvs/emboss/apps/needle(dot)html) canbe used to find the optimum alignment (including gaps) of two sequencesalong their entire length—a “Global alignment”. Default parameters forNeedleman-Wunsch algorithm (EMBOSS-6.0.1) include: gapopen=10;gapextend=0.5; datafile=EBLOSUM62; brief=YES.

According to some embodiments of the invention, the parameters used withthe EMBOSS-6.0.1 tool (for protein-protein comparison) include:gapopen=8; gapextend=2; datafile=EBLOSUM62; brief=YES.

According to some embodiments of the invention, the threshold used todetermine homology using the EMBOSS-6.0.1 Needleman-Wunsch algorithm is80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%,94%, 95%, 96%, 97%, 98%, 99%, or 100%.

When starting from a polypeptide sequence and comparing topolynucleotide sequences, the OneModel FramePlus algorithm [Halperin,E., Faigler, S. and Gill-More, R. (1999)—FramePlus: aligning DNA toprotein sequences. Bioinformatics, 15, 867-873) (available frombiocceleration(dot)com/Products(dot)html] can be used with followingdefault parameters: model=frame+_p2n.model mode=local.

According to some embodiments of the invention, the parameters used withthe OneModel FramePlus algorithm are model=frame+_p2n.model,mode=qglobal.

According to some embodiments of the invention, the threshold used todetermine homology using the OneModel FramePlus algorithm is 80%, 81%,82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%,96%, 97%, 98%, 99%, or 100%.

When starting with a polynucleotide sequence and comparing to otherpolynucleotide sequences the EMBOSS-6.0.1 Needleman-Wunsch algorithm(available fromemboss(dot)sourceforge(dot)net/apps/cvs/emboss/apps/needle(dot)html) canbe used with the following default parameters: (EMBOSS-6.0.1)gapopen=10; gapextend=0.5; datafile=EDNAFULL; brief=YES.

According to some embodiments of the invention, the parameters used withthe EMBOSS-6.0.1 Needleman-Wunsch algorithm are gapopen=10;gapextend=0.2; datafile=EDNAFULL; brief=YES.

According to some embodiments of the invention, the threshold used todetermine homology using the EMBOSS-6.0.1 Needleman-Wunsch algorithm forcomparison of polynucleotides with polynucleotides is 80%, 81%, 82%,83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%,97%, 98%, 99%, or 100%.

According to some embodiment, determination of the degree of homologyfurther requires employing the Smith-Waterman algorithm (forprotein-protein comparison or nucleotide-nucleotide comparison).

Default parameters for GenCore 6.0 Smith-Waterman algorithm include:model=sw.model.

According to some embodiments of the invention, the threshold used todetermine homology using the Smith-Waterman algorithm is 80%, 81%, 82%,83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%,97%, 98%, 99%, or 100%.

According to some embodiments of the invention, the global homology isperformed on sequences which are pre-selected by local homology to thepolypeptide or polynucleotide of interest (e.g., 60% identity over 60%of the sequence length), prior to performing the global homology to thepolypeptide or polynucleotide of interest (e.g., 80% global homology onthe entire sequence). For example, homologous sequences are selectedusing the BLAST software with the Blastp and tBlastn algorithms asfilters for the first stage, and the needle (EMBOSS package) or Frame+algorithm alignment for the second stage. Local identity (Blastalignments) is defined with a very permissive cutoff—60% Identity on aspan of 60% of the sequences lengths because it is used only as a filterfor the global alignment stage. In this specific embodiment (when thelocal identity is used), the default filtering of the Blast package isnot utilized (by setting the parameter “−F F”).

In the second stage, homologs are defined based on a global identity ofat least 80% to the core gene polypeptide sequence.

According to some embodiments of the invention, two distinct forms forfinding the optimal global alignment for protein or nucleotide sequencesare used:

1. Between Two Proteins (Following the Blastp Filter):

EMBOSS-6.0.1 Needleman-Wunsch algorithm with the following modifiedparameters: gapopen=8 gapextend=2. The rest of the parameters areunchanged from the default options listed here:

Standard (Mandatory) Qualifiers:

-   -   [-asequence] sequence Sequence filename and optional format, or        reference (input USA)    -   [-bsequence] seqall Sequence(s) filename and optional format, or        reference (input USA)

-gapopen float [10.0 for any sequence]. The gap open penalty is thescore taken away when a gap is created. The best value depends on thechoice of comparison matrix. The default value assumes you are using theEBLOSUM62 matrix for protein sequences, and the EDNAFULL matrix fornucleotide sequences. (Floating point number from 1.0 to 100.0)

-gapextend float [0.5 for any sequence]. The gap extension, penalty isadded to the standard gap penalty for each base or residue in the gap.This is how long gaps are penalized. Usually you will expect a few longgaps rather than many short gaps, so the gap extension penalty should belower than the gap penalty. An exception is where one or both sequencesare single reads with possible sequencing errors in which case you wouldexpect many single base gaps. You can get this result by setting the gapopen penalty to zero (or very low) and using the gap extension penaltyto control gap scoring. (Floating point number from 0.0 to 10.0)

-   -   [-outfile] align [*.needle] Output alignment file name

Additional (Optional) Qualifiers:

-datafile matrixf [EBLOSUM62 for protein, EDNAFULL for DNA]. This is thescoring matrix file used when comparing sequences. By default it is thefile ‘EBLOSUM62’ (for proteins) or the file ‘EDNAFULL’ (for nucleicsequences). These files are found in the ‘data’ directory of the EMBOSSinstallation.

Advanced (Unprompted) Qualifiers:

-   -   -[no]brief boolean [Y] Brief identity and similarity

Associated Qualifiers:

-   -   “-asequence” associated qualifiers    -   -sbegin1 integer Start of the sequence to be used    -   -send1 integer End of the sequence to be used    -   -sreverse1 boolean Reverse (if DNA)    -   -sask1 boolean Ask for begin/end/reverse    -   -snucleotide1 boolean Sequence is nucleotide    -   -sprotein1 boolean Sequence is protein    -   -slower1 boolean Make lower case    -   -supper1 boolean Make upper case    -   -sformat1 string Input sequence format    -   -sdbname1 string Database name    -   -sid1 string Entryname    -   -ufo1 string UFO features    -   -fformat1 string Features format    -   -fopenfile1 string Features file name    -   “-bsequence” associated qualifiers    -   -sbegin2 integer Start of each sequence to be used    -   -send2 integer End of each sequence to be used    -   -sreverse2 boolean Reverse (if DNA)    -   -sask2 boolean Ask for begin/end/reverse    -   -snucleotide2 boolean Sequence is nucleotide    -   -sprotein2 boolean Sequence is protein    -   -slower2 boolean Make lower case    -   -supper2 boolean Make upper case    -   -sformat2 string Input sequence format    -   -sdbname2 string Database name    -   -sid2 string Entryname    -   -ufo2 string UFO features    -   -fformat2 string Features format    -   -fopenfile2 string Features file name    -   “-outfile” associated qualifiers    -   -aformat3 string Alignment format    -   -aextension3 string File name extension    -   -adirectory3 string Output directory    -   -aname3 string Base file name    -   -awidth3 integer Alignment width    -   -aaccshow3 boolean Show accession number in the header    -   -adesshow3 boolean Show description in the header    -   -ausashow3 boolean Show the full USA in the alignment    -   -aglobal3 boolean Show the full sequence in alignment

General Qualifiers:

-   -   -auto boolean Turn off prompts    -   -stdout boolean Write first file to standard output    -   -filter boolean Read first file from standard input, write first        file to standard output    -   -options boolean Prompt for standard and additional values    -   -debug boolean Write debug output to program.dbg    -   -verbose boolean Report some/full command line options    -   -help boolean Report command line options. More information on        associated and general qualifiers can be found with -help        -verbose    -   -warning boolean Report warnings    -   -error boolean Report errors    -   -fatal boolean Report fatal errors    -   -die boolean Report dying program messages

2. Between a Protein Sequence and a Nucleotide Sequence (Following thetblastn Filter):

GenCore 6.0 OneModel application utilizing the Frame+ algorithm with thefollowing parameters: model=frame+_p2n.model mode=qglobal-q=protein.sequence -db=nucleotide.sequence. The rest of the parametersare unchanged from the default options:

Usage:

-   -   om -model=<model_fname>[-q=]query [-db=]database [options]    -   -model=<model_fname> Specifies the model that you want to run.        All models supplied by Compugen are located in the directory        $CGNROOT/models/.

Valid Command Line Parameters:

-   -   -dev=<dev_name> Selects the device to be used by the        application.        -   Valid devices are:        -   bic—Bioccelerator (valid for SW, XSW, FRAME_N2P, and            FRAME_P2N models).        -   xlg—BioXL/G (valid for all models except XSW).        -   xlp—BioXL/P (valid for SW, FRAME+_N2P, and FRAME_P2N            models).        -   xlh—BioXL/H (valid for SW, FRAME+_N2P, and FRAME_P2N            models).        -   soft—Software device (for all models).            -q=<query> Defines the query set. The query can be a            sequence file or a database reference. You can specify a            query by its name or by accession number. The format is            detected automatically. However, you may specify a format            using the -qfmt parameter. If you do not specify a query,            the program prompts for one. If the query set is a database            reference, an output file is produced for each sequence in            the query.            -db=<database name> Chooses the database set. The database            set can be a sequence file or a database reference. The            database format is detected automatically. However, you may            specify a format using -dfmt parameter.            -qacc Add this parameter to the command line if you specify            query using accession numbers.            -dacc Add this parameter to the command line if you specify            a database using accession numbers.            -dfmt/-qfmt=<format_type> Chooses the database/query format            type. Possible formats are:    -   fasta—fasta with seq type auto-detected.    -   fastap—fasta protein seq.    -   fastan—fasta nucleic seq.    -   gcg—gcg format, type is auto-detected.    -   gcg9seq—gcg9 format, type is auto-detected.    -   gcg9seqp—gcg9 format protein seq.    -   gcg9seqn—gcg9 format nucleic seq.    -   nbrf—nbrf seq, type is auto-detected.    -   nbrfp—nbrf protein seq.    -   nbrfn—nbrf nucleic seq.    -   embl—embl and swissprot format.    -   genbank—genbank format (nucleic).    -   blast—blast format.    -   nbrf gcg—nbrf-gcg seq, type is auto-detected.    -   nbrfgcgp—nbrf-gcg protein seq.    -   nbrfgcgn—nbrf-gcg nucleic seq.    -   raw—raw ascii sequence, type is auto-detected.    -   rawp—raw ascii protein sequence.    -   rawn—raw ascii nucleic sequence.    -   pir—pir codata format, type is auto-detected.    -   profile—gcg profile (valid only for -qfmt    -   in SW, XSW, FRAME_P2N, and FRAME+_P2N).        -out=<out_fname> The name of the output file.        -suffix=<name> The output file name suffix.        -gapop=<n> Gap open penalty. This parameter is not valid for        FRAME+. For        FrameSearch the default is 12.0. For other searches the default        is 10.0.        -gapext=<n> Gap extend penalty. This parameter is not valid for        FRAME+. For FrameSearch the default is 4.0. For other models:        the default for protein searches is 0.05, and the default for        nucleic searches is 1.0.        -qgapop=<n> The penalty for opening a gap in the query sequence.        The default is 10.0. Valid for XSW.        -qgapext=<n> The penalty for extending a gap in the query        sequence. The default is 0.05. Valid for XSW.        -start=<n> The position in the query sequence to begin the        search.        -end=<n> The position in the query sequence to stop the search.        -qtrans Performs a translated search, relevant for a nucleic        query against a protein database. The nucleic query is        translated to six reading frames and a result is given for each        frame.

Valid for SW and XSW.

-dtrans Performs a translated search, relevant for a protein queryagainst a DNA database. Each database entry is translated to six readingframes and a result is given for each frame.

Valid for SW and XSW.

Note: “-qtrans” and “-dtrans” options are mutually exclusive.-matrix=<matrix_file> Specifies the comparison matrix to be used in thesearch. The matrix must be in the BLAST format. If the matrix file isnot located in $CGNROOT/tables/matrix, specify the full path as thevalue of the -matrix parameter.-trans=<transtab_name> Translation table. The default location for thetable is $CGNROOT/tables/trans.-onestrand Restricts the search to just the top strand of thequery/database nucleic sequence.-list=<n> The maximum size of the output hit list. The default is 50.-docalign=<n> The number of documentation lines preceding eachalignment. The default is 10.-thr_score=<score_name> The score that places limits on the display ofresults. Scores that are smaller than -thr_min value or larger than-thr_max value are not shown. Valid options are: quality.

-   -   zscore.    -   escore.        -thr_max=<n> The score upper threshold. Results that are larger        than -thr_max value are not shown.        -thr_min=<n> The score lower threshold. Results that are lower        than -thr_min value are not shown.        -align=<n> The number of alignments reported in the output file.        -noalign Do not display alignment.        Note: “-align” and “-noalign” parameters are mutually exclusive.        -outfmt=<format_name> Specifies the output format type. The        default format is PFS.        Possible values are:    -   PFS—PFS text format    -   FASTA—FASTA text format    -   BLAST—BLAST text format        -nonorm Do not perform score normalization.        -norm=<norm_name> Specifies the normalization method. Valid        options are:    -   log—logarithm normalization.    -   std—standard normalization.    -   stat—Pearson statistical method.        Note: “-nonorm” and “-norm” parameters cannot be used together.        Note: Parameters -xgapop, -xgapext, -fgapop, -fgapext, -ygapop,        -ygapext, -delop, and -delext apply only to FRAME+.        -xgapop=<n> The penalty for opening a gap when inserting a codon        (triplet). The default is 12.0.        -xgapext=<n> The penalty for extending a gap when inserting a        codon (triplet). The default is 4.0.        -ygapop=<n> The penalty for opening a gap when deleting an amino        acid. The default is 12.0.        -ygapext=<n> The penalty for extending a gap when deleting an        amino acid. The default is 4.0.        -fgapop=<n> The penalty for opening a gap when inserting a DNA        base. The default is 6.0.        -fgapext=<n> The penalty for extending a gap when inserting a        DNA base. The default is 7.0.        -delop=<n> The penalty for opening a gap when deleting a DNA        base. The default is 6.0.        -delext=<n> The penalty for extending a gap when deleting a DNA        base. The default is 7.0.        -silent No screen output is produced.        -host=<host_name> The name of the host on which the server runs.        By default, the application uses the host specified in the file        $CGNROOT/cgnhosts.        -wait Do not go to the background when the device is busy. This        option is not relevant for the Parseq or Soft pseudo device.        -batch Run the job in the background. When this option is        specified, the file “$CGNROOT/defaults/batch.defaults” is used        for choosing the batch command. If this file does not exist, the        command “at now” is used to run the job.        Note: “-batch” and “-wait” parameters are mutually exclusive.        -version Prints the software version number.        -help Displays this help message. To get more specific help        type:    -   “om -model=<model_fname>-help”.

According to some embodiments the homology is a local homology or alocal identity.

Local alignments tools include, but are not limited to the BlastP,BlastN, BlastX or TBLASTN software of the National Center ofBiotechnology Information (NCBI), FASTA, and the Smith-Watermanalgorithm

A tblastn search allows the comparison between a protein sequence to thesix-frame translations of a nucleotide database. It can be a veryproductive way of finding homologous protein coding regions inunannotated nucleotide sequences such as expressed sequence tags (ESTs)and draft genome records (HTG), located in the BLAST databases est andhtgs, respectively.

Default parameters for blastp include: Max target sequences: 100;Expected threshold: e⁻⁵; Word size: 3; Max matches in a query range: 0;Scoring parameters: Matrix—BLOSUM62; filters and masking: Filter—lowcomplexity regions.

Local alignments tools, which can be used include, but are not limitedto, the tBLASTX algorithm, which compares the six-frame conceptualtranslation products of a nucleotide query sequence (both strands)against a protein sequence database. Default parameters include: Maxtarget sequences: 100; Expected threshold: 10; Word size: 3; Max matchesin a query range: 0; Scoring parameters: Matrix—BLOSUM62; filters andmasking: Filter—low complexity regions.

According to some embodiments of the invention, the exogenouspolynucleotide of the invention encodes a polypeptide having an aminoacid sequence at least about 80%, at least about 81%, at least about82%, at least about 83%, at least about 84%, at least about 85%, atleast about 86%, at least about 87%, at least about 88%, at least about89%, at least about 90%, at least about 91%, at least about 92%, atleast about 93%, at least about 94%, at least about 95%, at least about96%, at least about 97%, at least about 98%, at least about 99%, or moresay 100% identical to the amino acid sequence selected from the groupconsisting of SEQ ID NOs: 713-716, 718-734, 737-741, 743-744, 746-765,767-784, 786-788, 790-795, 797, 810-811, 813-876, 878-889, 891-929,931-1021, 1029-1064, 1067-1074, 1076-1080, 1082-1088, 1091-1092,1094-1153, 9283-9526, 9536, 9550-9772, 9825, 9832, 9843-9881, 9899,9908, 9925-9988, 9990-10284, 10290-11275, 11278-11279, 11282-11284,11289-11295, 11297-11299, 11301, 11303-11305, 11308-11312, 11314, 11384,11386, 11394, 11400, 11407, 11416-11417, 11421, 11425-11426, 11429,11433, 11439-11441, 11443-11444, 11446-11447, 11449-11450, 11453-11455,11457, 11460, 11468-11469, 11471, 11475, 11482, 11485, 11488,11494-11496, 11500-11503, 11505-11506, 11510-11513, 11516-11525, 11530,11551, 11555, 11559, 11561, 11570-11571, 11582, 11589, 11605, 11612,11695, 11697, 11699-13027, 13057, 13066, 13091-13092, 13104, 13109,13116, 13119-13180, 13188, 13192-13327, 13329-13352, 13355-13929,13941-13942, 13946-14913, 14989-15034, 15037-15049, 15051-15072,15074-15221, 15229-15252, 15254-15272, 15281-15409, 15425, 15428-15434,and 15455-15722.

According to some embodiments of the invention, the exogenouspolynucleotide of the invention encodes a polypeptide having the aminoacid sequence selected from the group consisting of SEQ ID NOs: 713-735,737-741, 743-765, 767-795, 797, 809-1021, 1029-1064, 1067-1080,1082-1092, 1094-1153, 9276-9281, 9283-9532, 9534-9541, 9543-9545,9548-9774, 9776, 9778-9785, 9788-9791, 9793-9801, 9803, 9806-9807,9809-9820, 9822-9823, 9825-9838, 9840-9841, 9843-9881, 9889-9890,9893-9894, 9897-9899, 9901, 9904, 9906, 9908-9910, 9912-10285,10287-11276, 11278-11319, 11321, 11323, 11328-11330, 11333-11336,11339-11342, 11344-11355, 11357, 11359-11362, 11364-11366, 11369-13113,13115-13944, 13946-14913, 14915, 14917-14918, 14920-14921, 14923-14924,14927-14933, 14937, 14939-14940, 14942, 14944-14949, 14951, 14953,14955-14958, 14960-14962, 14964-14971, 14973, 14976, 14978-14979,14989-15221, 15225-15272, 15275-15410, 15412-15420, 15422-15423,15425-15426, 15428-15434, 15436, 15440-15441, 15443-15444, 15446,15448-15449, and 15451-15726.

According to some embodiments of the invention, the method of increasingyield, seed yield, biomass, growth rate, vigor, oil content, fiberyield, fiber quality, fiber length, photosynthetic capacity, abioticstress tolerance, and/or nitrogen use efficiency of a plant, is effectedby expressing within the plant an exogenous polynucleotide comprising anucleic acid sequence encoding a polypeptide at least at least about80%, at least about 81%, at least about 82%, at least about 83%, atleast about 84%, at least about 85%, at least about 86%, at least about87%, at least about 88%, at least about 89%, at least about 90%, atleast about 91%, at least about 92%, at least about 93%, at least about94%, at least about 95%, at least about 96%, at least about 97%, atleast about 98%, at least about 99%, or more say 100% identical to theamino acid sequence selected from the group consisting of SEQ ID NOs:713-716, 718-734, 737-741, 743-744, 746-765, 767-784, 786-788, 790-795,797, 810-811, 813-876, 878-889, 891-929, 931-1021, 1029-1064, 1067-1074,1076-1080, 1082-1088, 1091-1092, 1094-1153, 9283-9526, 9536, 9550-9772,9825, 9832, 9843-9881, 9899, 9908, 9925-9988, 9990-10284, 10290-11275,11278-11279, 11282-11284, 11289-11295, 11297-11299, 11301, 11303-11305,11308-11312, 11314, 11384, 11386, 11394, 11400, 11407, 11416-11417,11421, 11425-11426, 11429, 11433, 11439-11441, 11443-11444, 11446-11447,11449-11450, 11453-11455, 11457, 11460, 11468-11469, 11471, 11475,11482, 11485, 11488, 11494-11496, 11500-11503, 11505-11506, 11510-11513,11516-11525, 11530, 11551, 11555, 11559, 11561, 11570-11571, 11582,11589, 11605, 11612, 11695, 11697, 11699-13027, 13057, 13066,13091-13092, 13104, 13109, 13116, 13119-13180, 13188, 13192-13327,13329-13352, 13355-13929, 13941-13942, 13946-14913, 14989-15034,15037-15049, 15051-15072, 15074-15221, 15229-15252, 15254-15272,15281-15409, 15425, 15428-15434, and 15455-15722, thereby increasing theyield, seed yield, biomass, growth rate, vigor, oil content, fiberyield, fiber quality, fiber length, photosynthetic capacity, abioticstress tolerance, and/or nitrogen use efficiency of the plant.

According to some embodiments of the invention, the exogenouspolynucleotide encodes a polypeptide consisting of the amino acidsequence set forth by SEQ ID NO: 713-735, 737-741, 743-765, 767-795,797, 809-1021, 1029-1064, 1067-1080, 1082-1092, 1094-1153, 9276-9281,9283-9532, 9534-9541, 9543-9545, 9548-9774, 9776, 9778-9785, 9788-9791,9793-9801, 9803, 9806-9807, 9809-9820, 9822-9823, 9825-9838, 9840-9841,9843-9881, 9889-9890, 9893-9894, 9897-9899, 9901, 9904, 9906, 9908-9910,9912-10285, 10287-11276, 11278-11319, 11321, 11323, 11328-11330,11333-11336, 11339-11342, 11344-11355, 11357, 11359-11362, 11364-11366,11369-13113, 13115-13944, 13946-14913, 14915, 14917-14918, 14920-14921,14923-14924, 14927-14933, 14937, 14939-14940, 14942, 14944-14949, 14951,14953, 14955-14958, 14960-14962, 14964-14971, 14973, 14976, 14978-14979,14989-15221, 15225-15272, 15275-15410, 15412-15420, 15422-15423,15425-15426, 15428-15434, 15436, 15440-15441, 15443-15444, 15446,15448-15449, 15451-15725 or 15726.

According to an aspect of some embodiments of the invention, the methodof increasing yield, seed yield, biomass, growth rate, vigor, oilcontent, fiber yield, fiber quality, fiber length, photosyntheticcapacity, abiotic stress tolerance, and/or nitrogen use efficiency of aplant, is effected by expressing within the plant an exogenouspolynucleotide comprising a nucleic acid sequence encoding a polypeptidecomprising an amino acid sequence selected from the group consisting ofSEQ ID NOs: 713-735, 737-741, 743-765, 767-795, 797, 809-1021,1029-1064, 1067-1080, 1082-1092, 1094-1153, 9276-9281, 9283-9532,9534-9541, 9543-9545, 9548-9774, 9776, 9778-9785, 9788-9791, 9793-9801,9803, 9806-9807, 9809-9820, 9822-9823, 9825-9838, 9840-9841, 9843-9881,9889-9890, 9893-9894, 9897-9899, 9901, 9904, 9906, 9908-9910,9912-10285, 10287-11276, 11278-11319, 11321, 11323, 11328-11330,11333-11336, 11339-11342, 11344-11355, 11357, 11359-11362, 11364-11366,11369-13113, 13115-13944, 13946-14913, 14915, 14917-14918, 14920-14921,14923-14924, 14927-14933, 14937, 14939-14940, 14942, 14944-14949, 14951,14953, 14955-14958, 14960-14962, 14964-14971, 14973, 14976, 14978-14979,14989-15221, 15225-15272, 15275-15410, 15412-15420, 15422-15423,15425-15426, 15428-15434, 15436, 15440-15441, 15443-15444, 15446,15448-15449, and 15451-15726, thereby increasing the yield, seed yield,biomass, growth rate, vigor, oil content, fiber yield, fiber quality,fiber length, photosynthetic capacity, abiotic stress tolerance, and/ornitrogen use efficiency of the plant.

According to an aspect of some embodiments of the invention, there isprovided a method of increasing yield, seed yield, biomass, growth rate,vigor, oil content, fiber yield, fiber quality, fiber length,photosynthetic capacity, abiotic stress tolerance, and/or nitrogen useefficiency of a plant, comprising expressing within the plant anexogenous polynucleotide comprising a nucleic acid sequence encoding apolypeptide selected from the group consisting of SEQ ID NOs: 713-735,737-741, 743-765, 767-795, 797, 809-1021, 1029-1064, 1067-1080,1082-1092, 1094-1153, 9276-9281, 9283-9532, 9534-9541, 9543-9545,9548-9774, 9776, 9778-9785, 9788-9791, 9793-9801, 9803, 9806-9807,9809-9820, 9822-9823, 9825-9838, 9840-9841, 9843-9881, 9889-9890,9893-9894, 9897-9899, 9901, 9904, 9906, 9908-9910, 9912-10285,10287-11276, 11278-11319, 11321, 11323, 11328-11330, 11333-11336,11339-11342, 11344-11355, 11357, 11359-11362, 11364-11366, 11369-13113,13115-13944, 13946-14913, 14915, 14917-14918, 14920-14921, 14923-14924,14927-14933, 14937, 14939-14940, 14942, 14944-14949, 14951, 14953,14955-14958, 14960-14962, 14964-14971, 14973, 14976, 14978-14979,14989-15221, 15225-15272, 15275-15410, 15412-15420, 15422-15423,15425-15426, 15428-15434, 15436, 15440-15441, 15443-15444, 15446,15448-15449, and 15451-15726, thereby increasing the yield, seed yield,biomass, growth rate, vigor, oil content, fiber yield, fiber quality,fiber length, photosynthetic capacity, abiotic stress tolerance, and/ornitrogen use efficiency of the plant.

According to some embodiments of the invention, the exogenouspolynucleotide encodes a polypeptide consisting of the amino acidsequence set forth by SEQ ID NO: 713-735, 737-741, 743-765, 767-795,797, 809-1021, 1029-1064, 1067-1080, 1082-1092, 1094-1153, 9276-9281,9283-9532, 9534-9541, 9543-9545, 9548-9774, 9776, 9778-9785, 9788-9791,9793-9801, 9803, 9806-9807, 9809-9820, 9822-9823, 9825-9838, 9840-9841,9843-9881, 9889-9890, 9893-9894, 9897-9899, 9901, 9904, 9906, 9908-9910,9912-10285, 10287-11276, 11278-11319, 11321, 11323, 11328-11330,11333-11336, 11339-11342, 11344-11355, 11357, 11359-11362, 11364-11366,11369-13113, 13115-13944, 13946-14913, 14915, 14917-14918, 14920-14921,14923-14924, 14927-14933, 14937, 14939-14940, 14942, 14944-14949, 14951,14953, 14955-14958, 14960-14962, 14964-14971, 14973, 14976, 14978-14979,14989-15221, 15225-15272, 15275-15410, 15412-15420, 15422-15423,15425-15426, 15428-15434, 15436, 15440-15441, 15443-15444, 15446,15448-15449, 15451-15725 or 15726.

According to some embodiments of the invention the exogenouspolynucleotide comprises a nucleic acid sequence which is at least about80%, at least about 81%, at least about 82%, at least about 83%, atleast about 84%, at least about 85%, at least about 86%, at least about87%, at least about 88%, at least about 89%, at least about 90%, atleast about 91%, at least about 92%, at least about 93%, at least about93%, at least about 94%, at least about 95%, at least about 96%, atleast about 97%, at least about 98%, at least about 99%, e.g., 100%identical to the nucleic acid sequence selected from the groupconsisting of SEQ ID NOs: 4-7, 9-25, 28-32, 34-35, 37-56, 58-75, 77-79,81-86, 88, 101-102, 104-167, 169-180, 182-220, 222-312, 320-389, 391,395-398, 400-416, 419-423, 425-426, 428-447, 449-464, 466-468, 470-475,477, 490-491, 493-555, 557-568, 570-605, 607-696, 704-709, 1164-1439,1453, 1468-1733, 1788, 1795, 1806-1860, 1884, 1899, 1917-2324,2331-3501, 3504-3506, 3509-3511, 3518-3526, 3528-3530, 3532, 3534-3536,3540-3547, 3549, 3638, 3641-3643, 3652, 3661, 3663, 3668, 3671,3683-3684, 3689, 3695-3696, 3700-3702, 3708, 3715-3718, 3720-3721,3723-3724, 3726-3727, 3732-3733, 3735, 3737, 3740, 3750-3751, 3753,3757, 3764-3765, 3768, 3772, 3776, 3783-3785, 3789-3792, 3794-3795,3800-3803, 3806-3818, 3827, 3889, 3894, 3898, 3900, 3915-3916, 3936,3943, 3964, 3971, 4099, 4101, 4103-4245, 4247-6064, 6103, 6112,6137-6138, 6150, 6155, 6162, 6165-6237, 6245, 6249-6406, 6408-6434,6437-7124, 7140-7141, 7145-8305, 8387-8453, 8457-8472, 8474-8505,8507-8683, 8691-8720, 8722-8748, 8757-8898, 8915, 8918-8927, and8948-9271.

According to an aspect of some embodiments of the invention, there isprovided a method of increasing yield, seed yield, biomass, growth rate,vigor, oil content, fiber yield, fiber quality, fiber length,photosynthetic capacity, abiotic stress tolerance, and/or nitrogen useefficiency of a plant, comprising expressing within the plant anexogenous polynucleotide comprising a nucleic acid sequence at leastabout 80%, at least about 81%, at least about 82%, at least about 83%,at least about 84%, at least about 85%, at least about 86%, at leastabout 87%, at least about 88%, at least about 89%, at least about 90%,at least about 91%, at least about 92%, at least about 93%, at leastabout 93%, at least about 94%, at least about 95%, at least about 96%,at least about 97%, at least about 98%, at least about 99%, e.g., 100%identical to the nucleic acid sequence selected from the groupconsisting of SEQ ID NOs: 4-7, 9-25, 28-32, 34-35, 37-56, 58-75, 77-79,81-86, 88, 101-102, 104-167, 169-180, 182-220, 222-312, 320-389, 391,395-398, 400-416, 419-423, 425-426, 428-447, 449-464, 466-468, 470-475,477, 490-491, 493-555, 557-568, 570-605, 607-696, 704-709, 1164-1439,1453, 1468-1733, 1788, 1795, 1806-1860, 1884, 1899, 1917-2324,2331-3501, 3504-3506, 3509-3511, 3518-3526, 3528-3530, 3532, 3534-3536,3540-3547, 3549, 3638, 3641-3643, 3652, 3661, 3663, 3668, 3671,3683-3684, 3689, 3695-3696, 3700-3702, 3708, 3715-3718, 3720-3721,3723-3724, 3726-3727, 3732-3733, 3735, 3737, 3740, 3750-3751, 3753,3757, 3764-3765, 3768, 3772, 3776, 3783-3785, 3789-3792, 3794-3795,3800-3803, 3806-3818, 3827, 3889, 3894, 3898, 3900, 3915-3916, 3936,3943, 3964, 3971, 4099, 4101, 4103-4245, 4247-6064, 6103, 6112,6137-6138, 6150, 6155, 6162, 6165-6237, 6245, 6249-6406, 6408-6434,6437-7124, 7140-7141, 7145-8305, 8387-8453, 8457-8472, 8474-8505,8507-8683, 8691-8720, 8722-8748, 8757-8898, 8915, 8918-8927, and8948-9271, thereby increasing the yield, seed yield, biomass, growthrate, vigor, oil content, fiber yield, fiber quality, fiber length,photosynthetic capacity, abiotic stress tolerance, and/or nitrogen useefficiency of the plant.

According to some embodiments of the invention the exogenouspolynucleotide is at least about 80%, at least about 81%, at least about82%, at least about 83%, at least about 84%, at least about 85%, atleast about 86%, at least about 87%, at least about 88%, at least about89%, at least about 90%, at least about 91%, at least about 92%, atleast about 93%, at least about 93%, at least about 94%, at least about95%, at least about 96%, at least about 97%, at least about 98%, atleast about 99%, e.g., 100% identical to the polynucleotide selectedfrom the group consisting of SEQ ID NOs: 4-7, 9-25, 28-32, 34-35, 37-56,58-75, 77-79, 81-86, 88, 101-102, 104-167, 169-180, 182-220, 222-312,320-389, 391, 395-398, 400-416, 419-423, 425-426, 428-447, 449-464,466-468, 470-475, 477, 490-491, 493-555, 557-568, 570-605, 607-696,704-709, 1164-1439, 1453, 1468-1733, 1788, 1795, 1806-1860, 1884, 1899,1917-2324, 2331-3501, 3504-3506, 3509-3511, 3518-3526, 3528-3530, 3532,3534-3536, 3540-3547, 3549, 3638, 3641-3643, 3652, 3661, 3663, 3668,3671, 3683-3684, 3689, 3695-3696, 3700-3702, 3708, 3715-3718, 3720-3721,3723-3724, 3726-3727, 3732-3733, 3735, 3737, 3740, 3750-3751, 3753,3757, 3764-3765, 3768, 3772, 3776, 3783-3785, 3789-3792, 3794-3795,3800-3803, 3806-3818, 3827, 3889, 3894, 3898, 3900, 3915-3916, 3936,3943, 3964, 3971, 4099, 4101, 4103-4245, 4247-6064, 6103, 6112,6137-6138, 6150, 6155, 6162, 6165-6237, 6245, 6249-6406, 6408-6434,6437-7124, 7140-7141, 7145-8305, 8387-8453, 8457-8472, 8474-8505,8507-8683, 8691-8720, 8722-8748, 8757-8898, 8915, 8918-8927, and8948-9271.

According to some embodiments of the invention the exogenouspolynucleotide is set forth by SEQ ID NO: 4-86, 88, 100-312, 320-389,391, 395-475, 477, 489-696, 704-709, 1157-4245, 4247-8375, 8387-8683,8686-9274 or 9275.

According to some embodiments of the invention the method of increasingyield, seed yield, biomass, growth rate, vigor, oil content, fiberyield, fiber quality, fiber length, photosynthetic capacity, abioticstress tolerance, and/or nitrogen use efficiency of a plant furthercomprising selecting a plant having an increased yield, seed yield,biomass, growth rate, vigor, oil content, fiber yield, fiber quality,fiber length, photosynthetic capacity, abiotic stress tolerance, and/ornitrogen use efficiency as compared to the wild type plant of the samespecies which is grown under the same growth conditions.

It should be noted that selecting a transformed plant having anincreased trait as compared to a native (or non-transformed) plant grownunder the same growth conditions can be performed by selecting for thetrait, e.g., validating the ability of the transformed plant to exhibitthe increased trait using well known assays (e.g., seedling analyses,greenhouse assays) as is further described herein below.

According to some embodiments of the invention selecting is performedunder non-stress conditions.

According to some embodiments of the invention selecting is performedunder abiotic stress conditions.

According to some embodiments of the invention selecting is performedunder nitrogen limiting conditions.

According to an aspect of some embodiments of the invention, there isprovided a method of selecting a transformed plant having increasedyield, seed yield, biomass, growth rate, vigor, oil content, fiberyield, fiber quality, fiber length, photosynthetic capacity, abioticstress tolerance, and/or nitrogen use efficiency as compared to a wildtype plant of the same species which is grown under the same growthconditions, the method comprising:

(a) providing plants transformed with an exogenous polynucleotideencoding a polypeptide comprising an amino acid sequence at least about80%, at least about 81%, at least about 82%, at least about 83%, atleast about 84%, at least about 85%, at least about 86%, at least about87%, at least about 88%, at least about 89%, at least about 90%, atleast about 91%, at least about 92%, at least about 93%, at least about93%, at least about 94%, at least about 95%, at least about 96%, atleast about 97%, at least about 98%, at least about 99%, e.g., 100%homologous (e.g., having sequence similarity or sequence identity) tothe amino acid sequence selected from the group consisting of SEQ IDNOs: 713-716, 718-734, 737-741, 743-744, 746-765, 767-784, 786-788,790-795, 797, 810-811, 813-876, 878-889, 891-929, 931-1021, 1029-1064,1067-1074, 1076-1080, 1082-1088, 1091-1092, 1094-1153, 9283-9526, 9536,9550-9772, 9825, 9832, 9843-9881, 9899, 9908, 9925-9988, 9990-10284,10290-11275, 11278-11279, 11282-11284, 11289-11295, 11297-11299, 11301,11303-11305, 11308-11312, 11314, 11384, 11386, 11394, 11400, 11407,11416-11417, 11421, 11425-11426, 11429, 11433, 11439-11441, 11443-11444,11446-11447, 11449-11450, 11453-11455, 11457, 11460, 11468-11469, 11471,11475, 11482, 11485, 11488, 11494-11496, 11500-11503, 11505-11506,11510-11513, 11516-11525, 11530, 11551, 11555, 11559, 11561,11570-11571, 11582, 11589, 11605, 11612, 11695, 11697, 11699-13027,13057, 13066, 13091-13092, 13104, 13109, 13116, 13119-13180, 13188,13192-13327, 13329-13352, 13355-13929, 13941-13942, 13946-14913,14989-15034, 15037-15049, 15051-15072, 15074-15221, 15229-15252,15254-15272, 15281-15409, 15425, 15428-15434, and 15455-15722,

(b) selecting from the plants of step (a) a plant having increasedyield, seed yield, biomass, growth rate, vigor, oil content, fiberyield, fiber quality, fiber length, photosynthetic capacity, abioticstress tolerance, and/or nitrogen use efficiency (e.g., by selecting theplants for the increased trait),

thereby selecting the plant having increased yield, seed yield, biomass,growth rate, vigor, oil content, fiber yield, fiber quality, fiberlength, photosynthetic capacity, abiotic stress tolerance, and/ornitrogen use efficiency as compared to the wild type plant of the samespecies which is grown under the same growth conditions.

According to an aspect of some embodiments of the invention, there isprovided a method of selecting a transformed plant having increasedyield, seed yield, biomass, growth rate, vigor, oil content, fiberyield, fiber quality, fiber length, photosynthetic capacity, abioticstress tolerance, and/or nitrogen use efficiency as compared to a wildtype plant of the same species which is grown under the same growthconditions, the method comprising:

(a) providing plants transformed with an exogenous polynucleotide atleast about 80%, at least about 81%, at least about 82%, at least about83%, at least about 84%, at least about 85%, at least about 86%, atleast about 87%, at least about 88%, at least about 89%, at least about90%, at least about 91%, at least about 92%, at least about 93%, atleast about 93%, at least about 94%, at least about 95%, at least about96%, at least about 97%, at least about 98%, at least about 99%, e.g.,100% identical to the nucleic acid sequence selected from the groupconsisting of SEQ ID NOs: 4-7, 9-25, 28-32, 34-35, 37-56, 58-75, 77-79,81-86, 88, 101-102, 104-167, 169-180, 182-220, 222-312, 320-389, 391,395-398, 400-416, 419-423, 425-426, 428-447, 449-464, 466-468, 470-475,477, 490-491, 493-555, 557-568, 570-605, 607-696, 704-709, 1164-1439,1453, 1468-1733, 1788, 1795, 1806-1860, 1884, 1899, 1917-2324,2331-3501, 3504-3506, 3509-3511, 3518-3526, 3528-3530, 3532, 3534-3536,3540-3547, 3549, 3638, 3641-3643, 3652, 3661, 3663, 3668, 3671,3683-3684, 3689, 3695-3696, 3700-3702, 3708, 3715-3718, 3720-3721,3723-3724, 3726-3727, 3732-3733, 3735, 3737, 3740, 3750-3751, 3753,3757, 3764-3765, 3768, 3772, 3776, 3783-3785, 3789-3792, 3794-3795,3800-3803, 3806-3818, 3827, 3889, 3894, 3898, 3900, 3915-3916, 3936,3943, 3964, 3971, 4099, 4101, 4103-4245, 4247-6064, 6103, 6112,6137-6138, 6150, 6155, 6162, 6165-6237, 6245, 6249-6406, 6408-6434,6437-7124, 7140-7141, 7145-8305, 8387-8453, 8457-8472, 8474-8505,8507-8683, 8691-8720, 8722-8748, 8757-8898, 8915, 8918-8927, and8948-9271,

(b) selecting from the plants of step (a) a plant having increasedyield, seed yield, biomass, growth rate, vigor, oil content, fiberyield, fiber quality, fiber length, photosynthetic capacity, abioticstress tolerance, and/or nitrogen use efficiency,

thereby selecting the plant having increased yield, seed yield, biomass,growth rate, vigor, oil content, fiber yield, fiber quality, fiberlength, photosynthetic capacity, abiotic stress tolerance, and/ornitrogen use efficiency as compared to the wild type plant of the samespecies which is grown under the same growth conditions.

As used herein the term “polynucleotide” refers to a single or doublestranded nucleic acid sequence which is isolated and provided in theform of an RNA sequence, a complementary polynucleotide sequence (cDNA),a genomic polynucleotide sequence and/or a composite polynucleotidesequences (e.g., a combination of the above).

The term “isolated” refers to at least partially separated from thenatural environment e.g., from a plant cell.

As used herein the phrase “complementary polynucleotide sequence” refersto a sequence, which results from reverse transcription of messenger RNAusing a reverse transcriptase or any other RNA dependent DNA polymerase.Such a sequence can be subsequently amplified in vivo or in vitro usinga DNA dependent DNA polymerase.

As used herein the phrase “genomic polynucleotide sequence” refers to asequence derived (isolated) from a chromosome and thus it represents acontiguous portion of a chromosome.

As used herein the phrase “composite polynucleotide sequence” refers toa sequence, which is at least partially complementary and at leastpartially genomic. A composite sequence can include some exonalsequences required to encode the polypeptide of the present invention,as well as some intronic sequences interposing therebetween. Theintronic sequences can be of any source, including of other genes, andtypically will include conserved splicing signal sequences. Suchintronic sequences may further include cis acting expression regulatoryelements.

Nucleic acid sequences encoding the polypeptides of the presentinvention may be optimized for expression. Examples of such sequencemodifications include, but are not limited to, an altered G/C content tomore closely approach that typically found in the plant species ofinterest, and the removal of codons atypically found in the plantspecies commonly referred to as codon optimization.

The phrase “codon optimization” refers to the selection of appropriateDNA nucleotides for use within a structural gene or fragment thereofthat approaches codon usage within the plant of interest. Therefore, anoptimized gene or nucleic acid sequence refers to a gene in which thenucleotide sequence of a native or naturally occurring gene has beenmodified in order to utilize statistically-preferred orstatistically-favored codons within the plant. The nucleotide sequencetypically is examined at the DNA level and the coding region optimizedfor expression in the plant species determined using any suitableprocedure, for example as described in Sardana et al. (1996, Plant CellReports 15:677-681). In this method, the standard deviation of codonusage, a measure of codon usage bias, may be calculated by first findingthe squared proportional deviation of usage of each codon of the nativegene relative to that of highly expressed plant genes, followed by acalculation of the average squared deviation. The formula used is: 1SDCU=n=1 N[(Xn−Yn)/Yn]2/N, where Xn refers to the frequency of usage ofcodon n in highly expressed plant genes, where Yn to the frequency ofusage of codon n in the gene of interest and N refers to the totalnumber of codons in the gene of interest. A Table of codon usage fromhighly expressed genes of dicotyledonous plants is compiled using thedata of Murray et al. (1989, Nuc Acids Res. 17:477-498).

One method of optimizing the nucleic acid sequence in accordance withthe preferred codon usage for a particular plant cell type is based onthe direct use, without performing any extra statistical calculations,of codon optimization Tables such as those provided on-line at the CodonUsage Database through the NIAS (National Institute of AgrobiologicalSciences) DNA bank in Japan (kazusa (dot) or (dot) jp/codon/). The CodonUsage Database contains codon usage tables for a number of differentspecies, with each codon usage Table having been statisticallydetermined based on the data present in Genbank.

By using the above Tables to determine the most preferred or mostfavored codons for each amino acid in a particular species (for example,rice), a naturally-occurring nucleotide sequence encoding a protein ofinterest can be codon optimized for that particular plant species. Thisis effected by replacing codons that may have a low statisticalincidence in the particular species genome with corresponding codons, inregard to an amino acid, that are statistically more favored. However,one or more less-favored codons may be selected to delete existingrestriction sites, to create new ones at potentially useful junctions(5′ and 3′ ends to add signal peptide or termination cassettes, internalsites that might be used to cut and splice segments together to producea correct full-length sequence), or to eliminate nucleotide sequencesthat may negatively effect mRNA stability or expression.

The naturally-occurring encoding nucleotide sequence may already, inadvance of any modification, contain a number of codons that correspondto a statistically-favored codon in a particular plant species.Therefore, codon optimization of the native nucleotide sequence maycomprise determining which codons, within the native nucleotidesequence, are not statistically-favored with regards to a particularplant, and modifying these codons in accordance with a codon usage tableof the particular plant to produce a codon optimized derivative. Amodified nucleotide sequence may be fully or partially optimized forplant codon usage provided that the protein encoded by the modifiednucleotide sequence is produced at a level higher than the proteinencoded by the corresponding naturally occurring or native gene.Construction of synthetic genes by altering the codon usage is describedin for example PCT Patent Application 93/07278.

According to some embodiments of the invention, the exogenouspolynucleotide is a non-coding RNA.

As used herein the phrase ‘non-coding RNA” refers to an RNA moleculewhich does not encode an amino acid sequence (a polypeptide). Examplesof such non-coding RNA molecules include, but are not limited to, anantisense RNA, a pre-miRNA (precursor of a microRNA), or a precursor ofa Piwi-interacting RNA (piRNA).

Non-limiting examples of non-coding RNA polynucleotides are provided inSEQ ID NOs: 1810, 3292, 3297-3302, 4172, 4177, 4180-4183, 4185-4189,4193-4207, 4216-4235, 4245-4257, 4265-4283, 4285-4290, 4292-4311,4320-4324, 4327-4328, 4331-4334, 4337-4341, 4348-4360, 4363-4371,4373-4378, 4381, 4383-4391, 4393-4394, 4396, 4398-4404, 4406, 4408-4410,4413-4417, 4419-4421, 4424-4431, 4677, 4702, 4887, 5003-5004, 5107,5277, 5354, 5676, 5697, 5714, 6024, 6031, 6565-6566, 6958, 7117, 8233,8263, and 8667.

Thus, the invention encompasses nucleic acid sequences describedhereinabove; fragments thereof, sequences hybridizable therewith,sequences homologous thereto, sequences encoding similar polypeptideswith different codon usage, altered sequences characterized bymutations, such as deletion, insertion or substitution of one or morenucleotides, either naturally occurring or man induced, either randomlyor in a targeted fashion.

According to some embodiments of the invention, the exogenouspolynucleotide encodes a polypeptide comprising an amino acid sequenceat least 80%, at least about 81%, at least about 82%, at least about83%, at least about 84%, at least about 85%, at least about 86%, atleast about 87%, at least about 88%, at least about 89%, at least about90%, at least about 91%, at least about 92%, at least about 93%, atleast about 93%, at least about 94%, at least about 95%, at least about96%, at least about 97%, at least about 98%, at least about 99%, e.g.,100% identical to the amino acid sequence of a naturally occurring plantorthologue of the polypeptide selected from the group consisting of SEQID NOs: 713-735, 737-741, 743-765, 767-795, 797, 809-1021, 1029-1064,1067-1080, 1082-1092, 1094-1153, 9276-9281, 9283-9532, 9534-9541,9543-9545, 9548-9774, 9776, 9778-9785, 9788-9791, 9793-9801, 9803,9806-9807, 9809-9820, 9822-9823, 9825-9838, 9840-9841, 9843-9881,9889-9890, 9893-9894, 9897-9899, 9901, 9904, 9906, 9908-9910,9912-10285, 10287-11276, 11278-11319, 11321, 11323, 11328-11330,11333-11336, 11339-11342, 11344-11355, 11357, 11359-11362, 11364-11366,11369-13113, 13115-13944, 13946-14913, 14915, 14917-14918, 14920-14921,14923-14924, 14927-14933, 14937, 14939-14940, 14942, 14944-14949, 14951,14953, 14955-14958, 14960-14962, 14964-14971, 14973, 14976, 14978-14979,14989-15221, 15225-15272, 15275-15410, 15412-15420, 15422-15423,15425-15426, 15428-15434, 15436, 15440-15441, 15443-15444, 15446,15448-15449, and 15451-15726.

According to some embodiments of the invention, the polypeptidecomprising an amino acid sequence at least 80%, at least about 81%, atleast about 82%, at least about 83%, at least about 84%, at least about85%, at least about 86%, at least about 87%, at least about 88%, atleast about 89%, at least about 90%, at least about 91%, at least about92%, at least about 93%, at least about 93%, at least about 94%, atleast about 95%, at least about 96%, at least about 97%, at least about98%, at least about 99%, e.g., 100% identical to the amino acid sequenceof a naturally occurring plant orthologue of the polypeptide selectedfrom the group consisting of SEQ ID NOs: 713-735, 737-741, 743-765,767-795, 797, 809-1021, 1029-1064, 1067-1080, 1082-1092, 1094-1153,9276-9281, 9283-9532, 9534-9541, 9543-9545, 9548-9774, 9776, 9778-9785,9788-9791, 9793-9801, 9803, 9806-9807, 9809-9820, 9822-9823, 9825-9838,9840-9841, 9843-9881, 9889-9890, 9893-9894, 9897-9899, 9901, 9904, 9906,9908-9910, 9912-10285, 10287-11276, 11278-11319, 11321, 11323,11328-11330, 11333-11336, 11339-11342, 11344-11355, 11357, 11359-11362,11364-11366, 11369-13113, 13115-13944, 13946-14913, 14915, 14917-14918,14920-14921, 14923-14924, 14927-14933, 14937, 14939-14940, 14942,14944-14949, 14951, 14953, 14955-14958, 14960-14962, 14964-14971, 14973,14976, 14978-14979, 14989-15221, 15225-15272, 15275-15410, 15412-15420,15422-15423, 15425-15426, 15428-15434, 15436, 15440-15441, 15443-15444,15446, 15448-15449, and 15451-15726.

The invention provides an isolated polynucleotide comprising a nucleicacid sequence at least about 80%, at least about 81%, at least about82%, at least about 83%, at least about 84%, at least about 85%, atleast about 86%, at least about 87%, at least about 88%, at least about89%, at least about 90%, at least about 91%, at least about 92%, atleast about 93%, at least about 93%, at least about 94%, at least about95%, at least about 96%, at least about 97%, at least about 98%, atleast about 99%, e.g., 100% identical to the polynucleotide selectedfrom the group consisting of SEQ ID NOs: 4-7, 9-25, 28-32, 34-35, 37-56,58-75, 77-79, 81-86, 88, 101-102, 104-167, 169-180, 182-220, 222-312,320-389, 391, 395-398, 400-416, 419-423, 425-426, 428-447, 449-464,466-468, 470-475, 477, 490-491, 493-555, 557-568, 570-605, 607-696,704-709, 1164-1439, 1453, 1468-1733, 1788, 1795, 1806-1860, 1884, 1899,1917-2324, 2331-3501, 3504-3506, 3509-3511, 3518-3526, 3528-3530, 3532,3534-3536, 3540-3547, 3549, 3638, 3641-3643, 3652, 3661, 3663, 3668,3671, 3683-3684, 3689, 3695-3696, 3700-3702, 3708, 3715-3718, 3720-3721,3723-3724, 3726-3727, 3732-3733, 3735, 3737, 3740, 3750-3751, 3753,3757, 3764-3765, 3768, 3772, 3776, 3783-3785, 3789-3792, 3794-3795,3800-3803, 3806-3818, 3827, 3889, 3894, 3898, 3900, 3915-3916, 3936,3943, 3964, 3971, 4099, 4101, 4103-4245, 4247-6064, 6103, 6112,6137-6138, 6150, 6155, 6162, 6165-6237, 6245, 6249-6406, 6408-6434,6437-7124, 7140-7141, 7145-8305, 8387-8453, 8457-8472, 8474-8505,8507-8683, 8691-8720, 8722-8748, 8757-8898, 8915, 8918-8927, and8948-9271.

According to some embodiments of the invention the nucleic acid sequenceis capable of increasing yield, seed yield, biomass, growth rate, vigor,oil content, fiber yield, fiber quality, fiber length, photosyntheticcapacity, abiotic stress tolerance, nitrogen use efficiency and/or wateruse efficiency of a plant.

According to some embodiments of the invention the isolatedpolynucleotide comprising the nucleic acid sequence selected from thegroup consisting of SEQ ID NOs: 4-86, 88, 100-312, 320-389, 391,395-475, 477, 489-696, 704-709, 1157-4245, 4247-8375, 8387-8683, and8686-9275.

According to some embodiments of the invention the isolatedpolynucleotide is set forth by SEQ ID NO: 4-86, 88, 100-312, 320-389,391, 395-475, 477, 489-696, 704-709, 1157-4245, 4247-8375, 8387-8683,8686-9274 or 9275.

The invention provides an isolated polynucleotide comprising a nucleicacid sequence encoding a polypeptide which comprises an amino acidsequence at least about 80%, at least about 81%, at least about 82%, atleast about 83%, at least about 84%, at least about 85%, at least about86%, at least about 87%, at least about 88%, at least about 89%, atleast about 90%, at least about 91%, at least about 92%, at least about93%, at least about 93%, at least about 94%, at least about 95%, atleast about 96%, at least about 97%, at least about 98%, at least about99%, or more say 100% homologous to the amino acid sequence selectedfrom the group consisting of SEQ ID NOs: 713-716, 718-734, 737-741,743-744, 746-765, 767-784, 786-788, 790-795, 797, 810-811, 813-876,878-889, 891-929, 931-1021, 1029-1064, 1067-1074, 1076-1080, 1082-1088,1091-1092, 1094-1153, 9283-9526, 9536, 9550-9772, 9825, 9832, 9843-9881,9899, 9908, 9925-9988, 9990-10284, 10290-11275, 11278-11279,11282-11284, 11289-11295, 11297-11299, 11301, 11303-11305, 11308-11312,11314, 11384, 11386, 11394, 11400, 11407, 11416-11417, 11421,11425-11426, 11429, 11433, 11439-11441, 11443-11444, 11446-11447,11449-11450, 11453-11455, 11457, 11460, 11468-11469, 11471, 11475,11482, 11485, 11488, 11494-11496, 11500-11503, 11505-11506, 11510-11513,11516-11525, 11530, 11551, 11555, 11559, 11561, 11570-11571, 11582,11589, 11605, 11612, 11695, 11697, 11699-13027, 13057, 13066,13091-13092, 13104, 13109, 13116, 13119-13180, 13188, 13192-13327,13329-13352, 13355-13929, 13941-13942, 13946-14913, 14989-15034,15037-15049, 15051-15072, 15074-15221, 15229-15252, 15254-15272,15281-15409, 15425, 15428-15434, and 15455-15722.

According to some embodiments of the invention the amino acid sequenceis capable of increasing yield, seed yield, biomass, growth rate, vigor,oil content, fiber yield, fiber quality, fiber length, photosyntheticcapacity, abiotic stress tolerance, nitrogen use efficiency and/or wateruse efficiency of a plant.

The invention provides an isolated polynucleotide comprising a nucleicacid sequence encoding a polypeptide which comprises the amino acidsequence selected from the group consisting of SEQ ID NOs: 713-735,737-741, 743-765, 767-795, 797, 809-1021, 1029-1064, 1067-1080,1082-1092, 1094-1153, 9276-9281, 9283-9532, 9534-9541, 9543-9545,9548-9774, 9776, 9778-9785, 9788-9791, 9793-9801, 9803, 9806-9807,9809-9820, 9822-9823, 9825-9838, 9840-9841, 9843-9881, 9889-9890,9893-9894, 9897-9899, 9901, 9904, 9906, 9908-9910, 9912-10285,10287-11276, 11278-11319, 11321, 11323, 11328-11330, 11333-11336,11339-11342, 11344-11355, 11357, 11359-11362, 11364-11366, 11369-13113,13115-13944, 13946-14913, 14915, 14917-14918, 14920-14921, 14923-14924,14927-14933, 14937, 14939-14940, 14942, 14944-14949, 14951, 14953,14955-14958, 14960-14962, 14964-14971, 14973, 14976, 14978-14979,14989-15221, 15225-15272, 15275-15410, 15412-15420, 15422-15423,15425-15426, 15428-15434, 15436, 15440-15441, 15443-15444, 15446,15448-15449, and 15451-15726.

According to an aspect of some embodiments of the invention, there isprovided a nucleic acid construct comprising the isolated polynucleotideof the invention, and a promoter for directing transcription of thenucleic acid sequence in a host cell.

The invention provides an isolated polypeptide comprising an amino acidsequence at least about 80%, at least about 81%, at least about 82%, atleast about 83%, at least about 84%, at least about 85%, at least about86%, at least about 87%, at least about 88%, at least about 89%, atleast about 90%, at least about 91%, at least about 92%, at least about93%, at least about 93%, at least about 94%, at least about 95%, atleast about 96%, at least about 97%, at least about 98%, at least about99%, or more say 100% homologous to an amino acid sequence selected fromthe group consisting of SEQ ID NOs: 713-716, 718-734, 737-741, 743-744,746-765, 767-784, 786-788, 790-795, 797, 810-811, 813-876, 878-889,891-929, 931-1021, 1029-1064, 1067-1074, 1076-1080, 1082-1088,1091-1092, 1094-1153, 9283-9526, 9536, 9550-9772, 9825, 9832, 9843-9881,9899, 9908, 9925-9988, 9990-10284, 10290-11275, 11278-11279,11282-11284, 11289-11295, 11297-11299, 11301, 11303-11305, 11308-11312,11314, 11384, 11386, 11394, 11400, 11407, 11416-11417, 11421,11425-11426, 11429, 11433, 11439-11441, 11443-11444, 11446-11447,11449-11450, 11453-11455, 11457, 11460, 11468-11469, 11471, 11475,11482, 11485, 11488, 11494-11496, 11500-11503, 11505-11506, 11510-11513,11516-11525, 11530, 11551, 11555, 11559, 11561, 11570-11571, 11582,11589, 11605, 11612, 11695, 11697, 11699-13027, 13057, 13066,13091-13092, 13104, 13109, 13116, 13119-13180, 13188, 13192-13327,13329-13352, 13355-13929, 13941-13942, 13946-14913, 14989-15034,15037-15049, 15051-15072, 15074-15221, 15229-15252, 15254-15272,15281-15409, 15425, 15428-15434, and 15455-15722.

According to some embodiments of the invention, the polypeptidecomprising an amino acid sequence selected from the group consisting ofSEQ ID NOs: 713-735, 737-741, 743-765, 767-795, 797, 809-1021,1029-1064, 1067-1080, 1082-1092, 1094-1153, 9276-9281, 9283-9532,9534-9541, 9543-9545, 9548-9774, 9776, 9778-9785, 9788-9791, 9793-9801,9803, 9806-9807, 9809-9820, 9822-9823, 9825-9838, 9840-9841, 9843-9881,9889-9890, 9893-9894, 9897-9899, 9901, 9904, 9906, 9908-9910,9912-10285, 10287-11276, 11278-11319, 11321, 11323, 11328-11330,11333-11336, 11339-11342, 11344-11355, 11357, 11359-11362, 11364-11366,11369-13113, 13115-13944, 13946-14913, 14915, 14917-14918, 14920-14921,14923-14924, 14927-14933, 14937, 14939-14940, 14942, 14944-14949, 14951,14953, 14955-14958, 14960-14962, 14964-14971, 14973, 14976, 14978-14979,14989-15221, 15225-15272, 15275-15410, 15412-15420, 15422-15423,15425-15426, 15428-15434, 15436, 15440-15441, 15443-15444, 15446,15448-15449, and 15451-15726.

According to some embodiments of the invention, the polypeptide is setforth by SEQ ID NO: 713-735, 737-741, 743-765, 767-795, 797, 809-1021,1029-1064, 1067-1080, 1082-1092, 1094-1153, 9276-9281, 9283-9532,9534-9541, 9543-9545, 9548-9774, 9776, 9778-9785, 9788-9791, 9793-9801,9803, 9806-9807, 9809-9820, 9822-9823, 9825-9838, 9840-9841, 9843-9881,9889-9890, 9893-9894, 9897-9899, 9901, 9904, 9906, 9908-9910,9912-10285, 10287-11276, 11278-11319, 11321, 11323, 11328-11330,11333-11336, 11339-11342, 11344-11355, 11357, 11359-11362, 11364-11366,11369-13113, 13115-13944, 13946-14913, 14915, 14917-14918, 14920-14921,14923-14924, 14927-14933, 14937, 14939-14940, 14942, 14944-14949, 14951,14953, 14955-14958, 14960-14962, 14964-14971, 14973, 14976, 14978-14979,14989-15221, 15225-15272, 15275-15410, 15412-15420, 15422-15423,15425-15426, 15428-15434, 15436, 15440-15441, 15443-15444, 15446,15448-15449, 15451-15725 or 15726.

The invention also encompasses fragments of the above describedpolypeptides and polypeptides having mutations, such as deletions,insertions or substitutions of one or more amino acids, either naturallyoccurring or man induced, either randomly or in a targeted fashion.

The term ‘“plant” as used herein encompasses a whole plant, a graftedplant, ancestor(s) and progeny of the plants and plant parts, includingseeds, shoots, stems, roots (including tubers), rootstock, scion, andplant cells, tissues and organs. The plant may be in any form includingsuspension cultures, embryos, meristematic regions, callus tissue,leaves, gametophytes, sporophytes, pollen, and microspores. Plants thatare particularly useful in the methods of the invention include allplants which belong to the superfamily Viridiplantae, in particularmonocotyledonous and dicotyledonous plants including a fodder or foragelegume, ornamental plant, food crop, tree, or shrub selected from thelist comprising Acacia spp., Acer spp., Actinidia spp., Aesculus spp.,Agathis australis, Albizia amara, Alsophila tricolor, Andropogon spp.,Arachis spp, Areca catechu, Astelia fragrans, Astragalus cicer, Baikiaeaplurijuga, Betula spp., Brassica spp., Bruguiera gymnorrhiza, Burkeaafricana, Butea frondosa, Cadaba farinosa, Calliandra spp, Camelliasinensis, Canna indica, Capsicum spp., Cassia spp., Centroema pubescens,Chacoomeles spp., Cinnamomum cassia, Coffea arabica, Colophospermummopane, Coronillia varia, Cotoneaster serotina, Crataegus spp., Cucumisspp., Cupressus spp., Cyathea dealbata, Cydonia oblonga, Cryptomeriajaponica, Cymbopogon spp., Cynthea dealbata, Cydonia oblonga, Dalbergiamonetaria, Davallia divaricata, Desmodium spp., Dicksonia squarosa,Dibeteropogon amplectens, Dioclea spp, Dolichos spp., Dorycnium rectum,Echinochloa pyramidalis, Ehraffia spp., Eleusine coracana, Eragrestisspp., Erythrina spp., Eucalypfus spp., Euclea schimperi, Eulaliavi/losa, Pagopyrum spp., Feijoa sellowlana, Fragaria spp., Flemingiaspp, Freycinetia banksli, Geranium thunbergii, GinAgo biloba, Glycinejavanica, Gliricidia spp, Gossypium hirsutum, Grevillea spp., Guibourtiacoleosperma, Hedysarum spp., Hemaffhia altissima, Heteropogon contoffus,Hordeum vulgare, Hyparrhenia rufa, Hypericum erectum, Hypeffheliadissolute, Indigo incamata, Iris spp., Leptarrhena pyrolifolia,Lespediza spp., Lettuca spp., Leucaena leucocephala, Loudetia simplex,Lotonus bainesli, Lotus spp., Macrotyloma axillare, Malus spp., Manihotesculenta, Medicago saliva, Metasequoia glyptostroboides, Musasapientum, Nicotianum spp., Onobrychis spp., Ornithopus spp., Oryzaspp., Peltophorum africanum, Pennisetum spp., Persea gratissima, Petuniaspp., Phaseolus spp., Phoenix canariensis, Phormium cookianum, Photiniaspp., Picea glauca, Pinus spp., Pisum sativam, Podocarpus totara,Pogonarthria fleckii, Pogonaffhria squarrosa, Populus spp., Prosopiscineraria, Pseudotsuga menziesii, Pterolobium stellatum, Pyrus communis,Quercus spp., Rhaphiolepsis umbellata, Rhopalostylis sapida, Rhusnatalensis, Ribes grossularia, Ribes spp., Robinia pseudoacacia, Rosaspp., Rubus spp., Salix spp., Schyzachyrium sanguineum, Sciadopitysvefficillata, Sequoia sempervirens, Sequoiadendron giganteum, Sorghumbicolor, Spinacia spp., Sporobolus fimbriatus, Stiburus alopecuroides,Stylosanthos humilis, Tadehagi spp, Taxodium distichum, Themedatriandra, Trifolium spp., Triticum spp., Tsuga heterophylla, Vacciniumspp., Vicia spp., Vitis vinifera, Watsonia pyramidata, Zantedeschiaaethiopica, Zea mays, amaranth, artichoke, asparagus, broccoli, Brusselssprouts, cabbage, canola, carrot, cauliflower, celery, collard greens,flax, kale, lentil, oilseed rape, okra, onion, potato, rice, soybean,straw, sugar beet, sugar cane, sunflower, tomato, squash tea, maize,wheat, barley, rye, oat, peanut, pea, lentil and alfalfa, cotton,rapeseed, canola, pepper, sunflower, tobacco, eggplant, eucalyptus, atree, an ornamental plant, a perennial grass and a forage crop.Alternatively algae and other non-Viridiplantae can be used for themethods of the present invention.

According to some embodiments of the invention, the plant used by themethod of the invention is a crop plant such as rice, maize, wheat,barley, peanut, potato, sesame, olive tree, palm oil, banana, soybean,sunflower, canola, sugarcane, alfalfa, millet, leguminosae (bean, pea),flax, lupinus, rapeseed, tobacco, poplar and cotton.

According to some embodiments of the invention the plant is adicotyledonous plant.

According to some embodiments of the invention the plant is amonocotyledonous plant.

According to some embodiments of the invention, there is provided aplant cell exogenously expressing the polynucleotide of some embodimentsof the invention, the nucleic acid construct of some embodiments of theinvention and/or the polypeptide of some embodiments of the invention.

According to some embodiments of the invention, expressing the exogenouspolynucleotide of the invention within the plant is effected bytransforming one or more cells of the plant with the exogenouspolynucleotide, followed by generating a mature plant from thetransformed cells and cultivating the mature plant under conditionssuitable for expressing the exogenous polynucleotide within the matureplant.

According to some embodiments of the invention, the transformation iseffected by introducing to the plant cell a nucleic acid construct whichincludes the exogenous polynucleotide of some embodiments of theinvention and at least one promoter for directing transcription of theexogenous polynucleotide in a host cell (a plant cell). Further detailsof suitable transformation approaches are provided hereinbelow.

As mentioned, the nucleic acid construct according to some embodimentsof the invention comprises a promoter sequence and the isolatedpolynucleotide of some embodiments of the invention.

According to some embodiments of the invention, the isolatedpolynucleotide is operably linked to the promoter sequence.

A coding nucleic acid sequence is “operably linked” to a regulatorysequence (e.g., promoter) if the regulatory sequence is capable ofexerting a regulatory effect on the coding sequence linked thereto.

As used herein, the term “promoter” refers to a region of DNA which liesupstream of the transcriptional initiation site of a gene to which RNApolymerase binds to initiate transcription of RNA. The promoter controlswhere (e.g., which portion of a plant) and/or when (e.g., at which stageor condition in the lifetime of an organism) the gene is expressed.

According to some embodiments of the invention, the promoter isheterologous to the isolated polynucleotide and/or to the host cell.

As used herein the phrase “heterologous promoter” refers to a promoterfrom a different species or from the same species but from a differentgene locus as of the isolated polynucleotide sequence.

According to some embodiments of the invention, the isolatedpolynucleotide is heterologous to the plant cell (e.g., thepolynucleotide is derived from a different plant species when comparedto the plant cell, thus the isolated polynucleotide and the plant cellare not from the same plant species).

Any suitable promoter sequence can be used by the nucleic acid constructof the present invention. Preferably the promoter is a constitutivepromoter, a tissue-specific, or an abiotic stress-inducible promoter.

According to some embodiments of the invention, the promoter is a plantpromoter, which is suitable for expression of the exogenouspolynucleotide in a plant cell.

Suitable promoters for expression in wheat include, but are not limitedto, Wheat SPA promoter (SEQ ID NO: 15727; Albanietal, Plant Cell, 9:171-184, 1997, which is fully incorporated herein by reference), wheatLMW (SEQ ID NO: 15728 (longer LMW promoter), and SEQ ID NO: 15729 (LMWpromoter) and HMW glutenin-1 (SEQ ID NO: 15730 (Wheat HMW glutenin-1longer promoter); and SEQ ID NO: 15731 (Wheat HMW glutenin-1 Promoter);Thomas and Flavell, The Plant Cell 2:1171-1180; Furtado et al., 2009Plant Biotechnology Journal 7:240-253, each of which is fullyincorporated herein by reference), wheat alpha, beta and gamma gliadins[e.g., SEQ ID NO: 15732 (wheat alpha gliadin, B genome, promoter); SEQID NO: 15733 (wheat gamma gliadin promoter); EMBO 3:1409-15, 1984, whichis fully incorporated herein by reference], wheat TdPR60 [SEQ ID NO:15734 (wheat TdPR60 longer promoter) or SEQ ID NO: 15735 (wheat TdPR60promoter); Kovalchuk et al., Plant Mol Biol 71:81-98, 2009, which isfully incorporated herein by reference], maize Ubl Promoter [cultivarNongda 105 (SEQ ID NO: 15736); GenBank: DQ141598.1; Taylor et al., PlantCell Rep 1993 12: 491-495, which is fully incorporated herein byreference; and cultivar B73 (SEQ ID NO: 15737); Christensen, A H, et al.Plant Mol. Biol. 18 (4), 675-689 (1992), which is fully incorporatedherein by reference]; rice actin 1 (SEQ ID NO: 15738; Mc Elroy et al.1990, The Plant Cell, Vol. 2, 163-171, which is fully incorporatedherein by reference), rice GOS2 [SEQ ID NO: 15739 (rice GOS2 longerpromoter) and SEQ ID NO: 15740 (rice GOS2 Promoter); De Pater et al.Plant J. 1992; 2: 837-44, which is fully incorporated herein byreference], arabidopsis Pho1 [SEQ ID NO: 15741 (arabidopsis Pho1Promoter); Hamburger et al., Plant Cell. 2002; 14: 889-902, which isfully incorporated herein by reference], ExpansinB promoters, e.g., riceExpB5 [SEQ ID NO: 15742 (rice ExpB5 longer promoter) and SEQ ID NO:15743 (rice ExpB5 promoter)] and Barley ExpB1 [SEQ ID NO: 15744 (barleyExpB1 Promoter), Won et al. Mol Cells. 2010; 30:369-76, which is fullyincorporated herein by reference], barley SS2 (sucrose synthase 2) [(SEQID NO: 15745), Guerin and Carbonero, Plant Physiology May 1997 vol. 114no. 1 55-62, which is fully incorporated herein by reference], and ricePG5a [SEQ ID NO: 15746, U.S. Pat. No. 7,700,835, Nakase et al., PlantMol Biol. 32:621-30, 1996, each of which is fully incorporated herein byreference].

Suitable constitutive promoters include, for example, CaMV 35S promoter[SEQ ID NO: 15747 (CaMV 35S (QFNC) Promoter); SEQ ID NO: 15748 (PJJ 35Sfrom Brachypodium); SEQ ID NO: 15749 (CaMV 35S (OLD) Promoter) (Odell etal., Nature 313:810-812, 1985)], Arabidopsis At6669 promoter (SEQ ID NO:15750 (Arabidopsis At6669 (OLD) Promoter); see PCT Publication No.WO04081173A2 or the new At6669 promoter (SEQ ID NO: 15751 (ArabidopsisAt6669 (NEW) Promoter)); maize Ubl Promoter [cultivar Nongda 105 (SEQ IDNO: 15736); GenBank: DQ141598.1; Taylor et al., Plant Cell Rep 1993 12:491-495, which is fully incorporated herein by reference; and cultivarB73 (SEQ ID NO: 15737); Christensen, A H, et al. Plant Mol. Biol. 18(4), 675-689 (1992), which is fully incorporated herein by reference];rice actin 1 (SEQ ID NO: 15738, McElroy et al., Plant Cell 2:163-171,1990); pEMU (Last et al., Theor. Appl. Genet. 81:581-588, 1991); CaMV19S (Nilsson et al., Physiol. Plant 100:456-462, 1997); rice GOS2 [SEQID NO: 15739 (rice GOS2 longer Promoter) and SEQ ID NO: 15740 (rice GOS2Promoter), de Pater et al, Plant J Nov; 2(6):837-44, 1992]; RBCSpromoter (SEQ ID NO: 15752); Rice cyclophilin (Bucholz et al, Plant MolBiol. 25(5):837-43, 1994); Maize H3 histone (Lepetit et al, Mol. Gen.Genet. 231: 276-285, 1992); Actin 2 (An et al, Plant J. 10(1); 107-121,1996) and Synthetic Super MAS (Ni et al., The Plant Journal 7: 661-76,1995). Other constitutive promoters include those in U.S. Pat. Nos.5,659,026, 5,608,149; 5,608,144; 5,604,121; 5,569,597: 5,466,785;5,399,680; 5,268,463; and 5,608,142.

Suitable tissue-specific promoters include, but not limited to,leaf-specific promoters [e.g., AT5G06690 (Thioredoxin) (high expression,SEQ ID NO: 15753), AT5G61520 (AtSTP3) (low expression, SEQ ID NO: 15754)described in Buttner et al 2000 Plant, Cell and Environment 23, 175-184,or the promoters described in Yamamoto et al., Plant J. 12:255-265,1997; Kwon et al., Plant Physiol. 105:357-67, 1994; Yamamoto et al.,Plant Cell Physiol. 35:773-778, 1994; Gotor et al., Plant J. 3:509-18,1993; Orozco et al., Plant Mol. Biol. 23:1129-1138, 1993; and Matsuokaet al., Proc. Natl. Acad. Sci. USA 90:9586-9590, 1993; as well asArabidopsis STP3 (AT5G61520) promoter (Buttner et al., Plant, Cell andEnvironment 23:175-184, 2000)], seed-preferred promoters [e.g., Napin(originated from Brassica napus which is characterized by a seedspecific promoter activity; Stuitje A. R. et. al. Plant BiotechnologyJournal 1 (4): 301-309; SEQ ID NO: 15755 (Brassica napus NAPIN Promoter)from seed specific genes (Simon, et al., Plant Mol. Biol. 5. 191, 1985;Scofield, et al., J. Biol. Chem. 262: 12202, 1987; Baszczynski, et al.,Plant Mol. Biol. 14: 633, 1990), rice PG5a (SEQ ID NO: 15746; U.S. Pat.No. 7,700,835), early seed development Arabidopsis BAN (AT1G61720) (SEQID NO: 15756, US 2009/0031450 A1), late seed development ArabidopsisABI3 (AT3G24650) (SEQ ID NO: 15757 (Arabidopsis ABI3 (AT3G24650) longerPromoter) or SEQ ID NO:15758 (Arabidopsis ABI3 (AT3G24650) Promoter))(Ng et al., Plant Molecular Biology 54: 25-38, 2004), Brazil Nut albumin(Pearson' et al., Plant Mol. Biol. 18: 235-245, 1992), legumin (Ellis,et al. Plant Mol. Biol. 10: 203-214, 1988), Glutelin (rice) (Takaiwa, etal., Mol. Gen. Genet. 208: 15-22, 1986; Takaiwa, et al., FEBS Letts.221: 43-47, 1987), Zein (Matzke et al Plant Mol Biol, 143). 323-321990), napA (Stalberg, et al, Planta 199: 515-519, 1996), Wheat SPA (SEQID NO: 15727; Albanietal, Plant Cell, 9: 171-184, 1997), sunfloweroleosin (Cummins, et al., Plant Mol. Biol. 19: 873-876, 1992)],endosperm specific promoters [e.g., wheat LMW (SEQ ID NO: 15728 (WheatLMW Longer Promoter), and SEQ ID NO: 15729 (Wheat LMW Promoter) and HMWglutenin-1 [(SEQ ID NO: 15730 (Wheat HMW glutenin-1 longer Promoter));and SEQ ID NO: 15731 (Wheat HMW glutenin-1 Promoter), Thomas andFlavell, The Plant Cell 2:1171-1180, 1990; Mol Gen Genet 216:81-90,1989; NAR 17:461-2), wheat alpha, beta and gamma gliadins (SEQ ID NO:15732 (wheat alpha gliadin (B genome) promoter); SEQ ID NO: 15733 (wheatgamma gliadin promoter); EMBO 3:1409-15, 1984), Barley ltrl promoter,barley B1, C, D hordein (Theor Appl Gen 98:1253-62, 1999; Plant J4:343-55, 1993; Mol Gen Genet 250:750-60, 1996), Barley DOF (Mena et al,The Plant Journal, 116(1): 53-62, 1998), Biz2 (EP99106056.7), Barley SS2(SEQ ID NO: 15745 (Barley SS2 Promoter); Guerin and Carbonero PlantPhysiology 114: 1 55-62, 1997), wheat Tarp60 (Kovalchuk et al., PlantMol Biol 71:81-98, 2009), barley D-hordein (D-Hor) and B-hordein (B-Hor)(Agnelo Furtado, Robert J. Henry and Alessandro Pellegrineschi (2009)],Synthetic promoter (Vicente-Carbajosa et al., Plant J. 13: 629-640,1998), rice prolamin NRP33, rice-globulin Glb-1 (Wu et al, Plant CellPhysiology 39(8) 885-889, 1998), rice alpha-globulin REB/OHP-1 (Nakaseet al. Plant Mol. Biol. 33: 513-S22, 1997), rice ADP-glucose PP (TransRes 6:157-68, 1997), maize ESR gene family (Plant J 12:235-46, 1997),sorgum gamma-kafirin (PMB 32:1029-35, 1996)], embryo specific promoters[e.g., rice OSH1 (Sato et al, Proc. Natl. Acad. Sci. USA, 93:8117-8122), KNOX (Postma-Haarsma et al, Plant Mol. Biol. 39:257-71,1999), rice oleosin (Wu et at, J. Biochem., 123:386, 1998)], andflower-specific promoters [e.g., AtPRP4, chalene synthase (chsA) (Vander Meer, et al., Plant Mol. Biol. 15, 95-109, 1990), LAT52 (Twell et alMol. Gen Genet. 217:240-245; 1989), Arabidopsis apetala-3 (Tilly et al.,Development. 125:1647-57, 1998), Arabidopsis APETALA 1 (AT1G69120, AP1)(SEQ ID NO: 15759 (Arabidopsis (AT1G69120) APETALA 1)) (Hempel et al.,Development 124:3845-3853, 1997)], and root promoters [e.g., the ROOTPpromoter [SEQ ID NO: 15760]; rice ExpB5 (SEQ ID NO: 15743 (rice ExpB5Promoter); or SEQ ID NO: 15742 (rice ExpB5 longer Promoter)) and barleyExpB1 promoters (SEQ ID NO: 15744) (Won et al. Mol. Cells 30: 369-376,2010); arabidopsis ATTPS-CIN (AT3G25820) promoter (SEQ ID NO: 15761;Chen et al., Plant Phys 135:1956-66, 2004); arabidopsis Pho1 promoter(SEQ ID NO: 15741, Hamburger et al., Plant Cell. 14: 889-902, 2002),which is also slightly induced by stress].

Suitable abiotic stress-inducible promoters include, but not limited to,salt-inducible promoters such as RD29A (Yamaguchi-Shinozalei et al.,Mol. Gen. Genet. 236:331-340, 1993); drought-inducible promoters such asmaize rab17 gene promoter (Pla et. al., Plant Mol. Biol. 21:259-266,1993), maize rab28 gene promoter (Busk et. al., Plant J. 11:1285-1295,1997) and maize Ivr2 gene promoter (Pelleschi et. al., Plant Mol. Biol.39:373-380, 1999); heat-inducible promoters such as heat tomatohsp80-promoter from tomato (U.S. Pat. No. 5,187,267).

The nucleic acid construct of some embodiments of the invention canfurther include an appropriate selectable marker and/or an origin ofreplication. According to some embodiments of the invention, the nucleicacid construct utilized is a shuttle vector, which can propagate both inE. coli (wherein the construct comprises an appropriate selectablemarker and origin of replication) and be compatible with propagation incells. The construct according to the present invention can be, forexample, a plasmid, a bacmid, a phagemid, a cosmid, a phage, a virus oran artificial chromosome.

The nucleic acid construct of some embodiments of the invention can beutilized to stably or transiently transform plant cells. In stabletransformation, the exogenous polynucleotide is integrated into theplant genome and as such it represents a stable and inherited trait. Intransient transformation, the exogenous polynucleotide is expressed bythe cell transformed but it is not integrated into the genome and assuch it represents a transient trait.

There are various methods of introducing foreign genes into bothmonocotyledonous and dicotyledonous plants (Potrykus, I., Annu. Rev.Plant. Physiol., Plant. Mol. Biol. (1991) 42:205-225; Shimamoto et al.,Nature (1989) 338:274-276).

The principle methods of causing stable integration of exogenous DNAinto plant genomic DNA include two main approaches:

(i) Agrobacterium-mediated gene transfer: Klee et al. (1987) Annu. Rev.Plant Physiol. 38:467-486; Klee and Rogers in Cell Culture and SomaticCell Genetics of Plants, Vol. 6, Molecular Biology of Plant NuclearGenes, eds. Schell, J., and Vasil, L. K., Academic Publishers, SanDiego, Calif. (1989) p. 2-25; Gatenby, in Plant Biotechnology, eds.Kung, S. and Arntzen, C. J., Butterworth Publishers, Boston, Mass.(1989) p. 93-112.

(ii) Direct DNA uptake: Paszkowski et al., in Cell Culture and SomaticCell Genetics of Plants, Vol. 6, Molecular Biology of Plant NuclearGenes eds. Schell, J., and Vasil, L. K., Academic Publishers, San Diego,Calif. (1989) p. 52-68; including methods for direct uptake of DNA intoprotoplasts, Toriyama, K. et al. (1988) Bio/Technology 6:1072-1074. DNAuptake induced by brief electric shock of plant cells: Zhang et al.Plant Cell Rep. (1988) 7:379-384. Fromm et al. Nature (1986)319:791-793. DNA injection into plant cells or tissues by particlebombardment, Klein et al. Bio/Technology (1988) 6:559-563; McCabe et al.Bio/Technology (1988) 6:923-926; Sanford, Physiol. Plant. (1990)79:206-209; by the use of micropipette systems: Neuhaus et al., Theor.Appl. Genet. (1987) 75:30-36; Neuhaus and Spangenberg, Physiol. Plant.(1990) 79:213-217; glass fibers or silicon carbide whiskertransformation of cell cultures, embryos or callus tissue, U.S. Pat. No.5,464,765 or by the direct incubation of DNA with germinating pollen,DeWet et al. in Experimental Manipulation of Ovule Tissue, eds. Chapman,G. P. and Mantell, S. H. and Daniels, W. Longman, London, (1985) p.197-209; and Ohta, Proc. Natl. Acad. Sci. USA (1986) 83:715-719.

The Agrobacterium system includes the use of plasmid vectors thatcontain defined DNA segments that integrate into the plant genomic DNA.Methods of inoculation of the plant tissue vary depending upon the plantspecies and the Agrobacterium delivery system. A widely used approach isthe leaf disc procedure which can be performed with any tissue explantthat provides a good source for initiation of whole plantdifferentiation. See, e.g., Horsch et al. in Plant Molecular BiologyManual A5, Kluwer Academic Publishers, Dordrecht (1988) p. 1-9. Asupplementary approach employs the Agrobacterium delivery system incombination with vacuum infiltration. The Agrobacterium system isespecially viable in the creation of transgenic dicotyledonous plants.

There are various methods of direct DNA transfer into plant cells. Inelectroporation, the protoplasts are briefly exposed to a strongelectric field. In microinjection, the DNA is mechanically injecteddirectly into the cells using very small micropipettes. In microparticlebombardment, the DNA is adsorbed on microprojectiles such as magnesiumsulfate crystals or tungsten particles, and the microprojectiles arephysically accelerated into cells or plant tissues.

Following stable transformation plant propagation is exercised. The mostcommon method of plant propagation is by seed. Regeneration by seedpropagation, however, has the deficiency that due to heterozygositythere is a lack of uniformity in the crop, since seeds are produced byplants according to the genetic variances governed by Mendelian rules.Basically, each seed is genetically different and each will grow withits own specific traits. Therefore, it is preferred that the transformedplant be produced such that the regenerated plant has the identicaltraits and characteristics of the parent transgenic plant. Therefore, itis preferred that the transformed plant be regenerated bymicropropagation which provides a rapid, consistent reproduction of thetransformed plants.

Micropropagation is a process of growing new generation plants from asingle piece of tissue that has been excised from a selected parentplant or cultivar. This process permits the mass reproduction of plantshaving the preferred tissue expressing the fusion protein. The newgeneration plants which are produced are genetically identical to, andhave all of the characteristics of, the original plant. Micropropagationallows mass production of quality plant material in a short period oftime and offers a rapid multiplication of selected cultivars in thepreservation of the characteristics of the original transgenic ortransformed plant. The advantages of cloning plants are the speed ofplant multiplication and the quality and uniformity of plants produced.

Micropropagation is a multi-stage procedure that requires alteration ofculture medium or growth conditions between stages. Thus, themicropropagation process involves four basic stages: Stage one, initialtissue culturing; stage two, tissue culture multiplication; stage three,differentiation and plant formation; and stage four, greenhouseculturing and hardening. During stage one, initial tissue culturing, thetissue culture is established and certified contaminant-free. Duringstage two, the initial tissue culture is multiplied until a sufficientnumber of tissue samples are produced from the seedlings to meetproduction goals. During stage three, the tissue samples grown in stagetwo are divided and grown into individual plantlets. At stage four, thetransformed plantlets are transferred to a greenhouse for hardeningwhere the plants' tolerance to light is gradually increased so that itcan be grown in the natural environment.

According to some embodiments of the invention, the transgenic plantsare generated by transient transformation of leaf cells, meristematiccells or the whole plant.

Transient transformation can be effected by any of the direct DNAtransfer methods described above or by viral infection using modifiedplant viruses.

Viruses that have been shown to be useful for the transformation ofplant hosts include CaMV, Tobacco mosaic virus (TMV), brome mosaic virus(BMV) and Bean Common Mosaic Virus (BV or BCMV). Transformation ofplants using plant viruses is described in U.S. Pat. No. 4,855,237 (beangolden mosaic virus; BGV), EP-A 67,553 (TMV), Japanese PublishedApplication No. 63-14693 (TMV), EPA 194,809 (BV), EPA 278,667 (BV); andGluzman, Y. et al., Communications in Molecular Biology: Viral Vectors,Cold Spring Harbor Laboratory, New York, pp. 172-189 (1988). Pseudovirusparticles for use in expressing foreign DNA in many hosts, includingplants are described in WO 87/06261.

According to some embodiments of the invention, the virus used fortransient transformations is avirulent and thus is incapable of causingsevere symptoms such as reduced growth rate, mosaic, ring spots, leafroll, yellowing, streaking, pox formation, tumor formation and pitting.A suitable avirulent virus may be a naturally occurring avirulent virusor an artificially attenuated virus. Virus attenuation may be effectedby using methods well known in the art including, but not limited to,sub-lethal heating, chemical treatment or by directed mutagenesistechniques such as described, for example, by Kurihara and Watanabe(Molecular Plant Pathology 4:259-269, 2003), Gal-on et al. (1992),Atreya et al. (1992) and Huet et al. (1994).

Suitable virus strains can be obtained from available sources such as,for example, the American Type culture Collection (ATCC) or by isolationfrom infected plants. Isolation of viruses from infected plant tissuescan be effected by techniques well known in the art such as described,for example by Foster and Taylor, Eds. “Plant Virology Protocols: FromVirus Isolation to Transgenic Resistance (Methods in Molecular Biology(Humana Pr), Vol 81)”, Humana Press, 1998. Briefly, tissues of aninfected plant believed to contain a high concentration of a suitablevirus, preferably young leaves and flower petals, are ground in a buffersolution (e.g., phosphate buffer solution) to produce a virus infectedsap which can be used in subsequent inoculations.

Construction of plant RNA viruses for the introduction and expression ofnon-viral exogenous polynucleotide sequences in plants is demonstratedby the above references as well as by Dawson, W. O. et al., Virology(1989) 172:285-292; Takamatsu et al. EMBO J. (1987) 6:307-311; French etal. Science (1986) 231:1294-1297; Takamatsu et al. FEBS Letters (1990)269:73-76; and U.S. Pat. No. 5,316,931.

When the virus is a DNA virus, suitable modifications can be made to thevirus itself. Alternatively, the virus can first be cloned into abacterial plasmid for ease of constructing the desired viral vector withthe foreign DNA. The virus can then be excised from the plasmid. If thevirus is a DNA virus, a bacterial origin of replication can be attachedto the viral DNA, which is then replicated by the bacteria.Transcription and translation of this DNA will produce the coat proteinwhich will encapsidate the viral DNA. If the virus is an RNA virus, thevirus is generally cloned as a cDNA and inserted into a plasmid. Theplasmid is then used to make all of the constructions. The RNA virus isthen produced by transcribing the viral sequence of the plasmid andtranslation of the viral genes to produce the coat protein(s) whichencapsidate the viral RNA.

In one embodiment, a plant viral polynucleotide is provided in which thenative coat protein coding sequence has been deleted from a viralpolynucleotide, a non-native plant viral coat protein coding sequenceand a non-native promoter, preferably the subgenomic promoter of thenon-native coat protein coding sequence, capable of expression in theplant host, packaging of the recombinant plant viral polynucleotide, andensuring a systemic infection of the host by the recombinant plant viralpolynucleotide, has been inserted. Alternatively, the coat protein genemay be inactivated by insertion of the non-native polynucleotidesequence within it, such that a protein is produced. The recombinantplant viral polynucleotide may contain one or more additional non-nativesubgenomic promoters. Each non-native subgenomic promoter is capable oftranscribing or expressing adjacent genes or polynucleotide sequences inthe plant host and incapable of recombination with each other and withnative subgenomic promoters. Non-native (foreign) polynucleotidesequences may be inserted adjacent the native plant viral subgenomicpromoter or the native and a non-native plant viral subgenomic promotersif more than one polynucleotide sequence is included. The non-nativepolynucleotide sequences are transcribed or expressed in the host plantunder control of the subgenomic promoter to produce the desiredproducts.

In a second embodiment, a recombinant plant viral polynucleotide isprovided as in the first embodiment except that the native coat proteincoding sequence is placed adjacent one of the non-native coat proteinsubgenomic promoters instead of a non-native coat protein codingsequence.

In a third embodiment, a recombinant plant viral polynucleotide isprovided in which the native coat protein gene is adjacent itssubgenomic promoter and one or more non-native subgenomic promoters havebeen inserted into the viral polynucleotide. The inserted non-nativesubgenomic promoters are capable of transcribing or expressing adjacentgenes in a plant host and are incapable of recombination with each otherand with native subgenomic promoters. Non-native polynucleotidesequences may be inserted adjacent the non-native subgenomic plant viralpromoters such that the sequences are transcribed or expressed in thehost plant under control of the subgenomic promoters to produce thedesired product.

In a fourth embodiment, a recombinant plant viral polynucleotide isprovided as in the third embodiment except that the native coat proteincoding sequence is replaced by a non-native coat protein codingsequence.

The viral vectors are encapsidated by the coat proteins encoded by therecombinant plant viral polynucleotide to produce a recombinant plantvirus. The recombinant plant viral polynucleotide or recombinant plantvirus is used to infect appropriate host plants. The recombinant plantviral polynucleotide is capable of replication in the host, systemicspread in the host, and transcription or expression of foreign gene(s)(exogenous polynucleotide) in the host to produce the desired protein.

Techniques for inoculation of viruses to plants may be found in Fosterand Taylor, eds. “Plant Virology Protocols: From Virus Isolation toTransgenic Resistance (Methods in Molecular Biology (Humana Pr), Vol81)”, Humana Press, 1998; Maramorosh and Koprowski, eds. “Methods inVirology” 7 vols, Academic Press, New York 1967-1984; Hill, S. A.“Methods in Plant Virology”, Blackwell, Oxford, 1984; Walkey, D. G. A.“Applied Plant Virology”, Wiley, New York, 1985; and Kado and Agrawa,eds. “Principles and Techniques in Plant Virology”, VanNostrand-Reinhold, New York.

In addition to the above, the polynucleotide of the present inventioncan also be introduced into a chloroplast genome thereby enablingchloroplast expression.

A technique for introducing exogenous polynucleotide sequences to thegenome of the chloroplasts is known. This technique involves thefollowing procedures. First, plant cells are chemically treated so as toreduce the number of chloroplasts per cell to about one. Then, theexogenous polynucleotide is introduced via particle bombardment into thecells with the aim of introducing at least one exogenous polynucleotidemolecule into the chloroplasts. The exogenous polynucleotides selectedsuch that it is integratable into the chloroplast's genome viahomologous recombination which is readily effected by enzymes inherentto the chloroplast. To this end, the exogenous polynucleotide includes,in addition to a gene of interest, at least one polynucleotide stretchwhich is derived from the chloroplast's genome. In addition, theexogenous polynucleotide includes a selectable marker, which serves bysequential selection procedures to ascertain that all or substantiallyall of the copies of the chloroplast genomes following such selectionwill include the exogenous polynucleotide. Further details relating tothis technique are found in U.S. Pat. Nos. 4,945,050; and 5,693,507which are incorporated herein by reference. A polypeptide can thus beproduced by the protein expression system of the chloroplast and becomeintegrated into the chloroplast's inner membrane.

According to some embodiments, there is provided a method of improvingnitrogen use efficiency, yield, seed yield, growth rate, biomass, vigor,oil content, fiber yield, fiber quality, fiber length, photosyntheticcapacity, and/or abiotic stress tolerance of a grafted plant, the methodcomprising providing a scion that does not transgenically express apolynucleotide encoding a polypeptide at least 80% homologous to theamino acid sequence selected from the group consisting of SEQ ID NOs:713-735, 737-741, 743-765, 767-795, 797, 809-1021, 1029-1064, 1067-1080,1082-1092, 1094-1153, 9276-9281, 9283-9532, 9534-9541, 9543-9545,9548-9774, 9776, 9778-9785, 9788-9791, 9793-9801, 9803, 9806-9807,9809-9820, 9822-9823, 9825-9838, 9840-9841, 9843-9881, 9889-9890,9893-9894, 9897-9899, 9901, 9904, 9906, 9908-9910, 9912-10285,10287-11276, 11278-11319, 11321, 11323, 11328-11330, 11333-11336,11339-11342, 11344-11355, 11357, 11359-11362, 11364-11366, 11369-13113,13115-13944, 13946-14913, 14915, 14917-14918, 14920-14921, 14923-14924,14927-14933, 14937, 14939-14940, 14942, 14944-14949, 14951, 14953,14955-14958, 14960-14962, 14964-14971, 14973, 14976, 14978-14979,14989-15221, 15225-15272, 15275-15410, 15412-15420, 15422-15423,15425-15426, 15428-15434, 15436, 15440-15441, 15443-15444, 15446,15448-15449, and 15451-15726 and a plant rootstock that transgenicallyexpresses a polynucleotide encoding a polypeptide at least about 80%, atleast about 81%, at least about 82%, at least about 83%, at least about84%, at least about 85%, at least about 86%, at least about 87%, atleast about 88%, at least about 89%, at least about 90%, at least about91%, at least about 92%, at least about 93%, at least about 93%, atleast about 94%, at least about 95%, at least about 96%, at least about97%, at least about 98%, at least about 99%, e.g., 100% homologous (oridentical) to the amino acid sequence selected from the group consistingof SEQ ID NOs: 713-716, 718-734, 737-741, 743-744, 746-765, 767-784,786-788, 790-795, 797, 810-811, 813-876, 878-889, 891-929, 931-1021,1029-1064, 1067-1074, 1076-1080, 1082-1088, 1091-1092, 1094-1153,9283-9526, 9536, 9550-9772, 9825, 9832, 9843-9881, 9899, 9908,9925-9988, 9990-10284, 10290-11275, 11278-11279, 11282-11284,11289-11295, 11297-11299, 11301, 11303-11305, 11308-11312, 11314, 11384,11386, 11394, 11400, 11407, 11416-11417, 11421, 11425-11426, 11429,11433, 11439-11441, 11443-11444, 11446-11447, 11449-11450, 11453-11455,11457, 11460, 11468-11469, 11471, 11475, 11482, 11485, 11488,11494-11496, 11500-11503, 11505-11506, 11510-11513, 11516-11525, 11530,11551, 11555, 11559, 11561, 11570-11571, 11582, 11589, 11605, 11612,11695, 11697, 11699-13027, 13057, 13066, 13091-13092, 13104, 13109,13116, 13119-13180, 13188, 13192-13327, 13329-13352, 13355-13929,13941-13942, 13946-14913, 14989-15034, 15037-15049, 15051-15072,15074-15221, 15229-15252, 15254-15272, 15281-15409, 15425, 15428-15434,and 15455-15722 (e.g., in a constitutive, tissue specific or inducible,e.g., in an abiotic stress responsive manner), thereby improving thenitrogen use efficiency, yield, growth rate, biomass, vigor, oilcontent, seed yield, fiber yield, fiber quality, fiber length,photosynthetic capacity, and/or abiotic stress tolerance of the graftedplant.

In some embodiments, the plant scion is non-transgenic.

Several embodiments relate to a grafted plant exhibiting improvednitrogen use efficiency, yield, growth rate, biomass, vigor, oilcontent, seed yield, fiber yield, fiber quality, fiber length,photosynthetic capacity, and/or abiotic stress tolerance, comprising ascion that does not transgenically express a polynucleotide encoding apolypeptide at least 80% homologous to the amino acid sequence selectedfrom the group consisting of SEQ ID NOs: 713-735, 737-741, 743-765,767-795, 797, 809-1021, 1029-1064, 1067-1080, 1082-1092, 1094-1153,9276-9281, 9283-9532, 9534-9541, 9543-9545, 9548-9774, 9776, 9778-9785,9788-9791, 9793-9801, 9803, 9806-9807, 9809-9820, 9822-9823, 9825-9838,9840-9841, 9843-9881, 9889-9890, 9893-9894, 9897-9899, 9901, 9904, 9906,9908-9910, 9912-10285, 10287-11276, 11278-11319, 11321, 11323,11328-11330, 11333-11336, 11339-11342, 11344-11355, 11357, 11359-11362,11364-11366, 11369-13113, 13115-13944, 13946-14913, 14915, 14917-14918,14920-14921, 14923-14924, 14927-14933, 14937, 14939-14940, 14942,14944-14949, 14951, 14953, 14955-14958, 14960-14962, 14964-14971, 14973,14976, 14978-14979, 14989-15221, 15225-15272, 15275-15410, 15412-15420,15422-15423, 15425-15426, 15428-15434, 15436, 15440-15441, 15443-15444,15446, 15448-15449, and 15451-15726 and a plant rootstock thattransgenically expresses a polynucleotide encoding a polypeptide atleast about 80%, at least about 81%, at least about 82%, at least about83%, at least about 84%, at least about 85%, at least about 86%, atleast about 87%, at least about 88%, at least about 89%, at least about90%, at least about 91%, at least about 92%, at least about 93%, atleast about 93%, at least about 94%, at least about 95%, at least about96%, at least about 97%, at least about 98%, at least about 99%, e.g.,100% homologous (or identical) to the amino acid sequence selected fromthe group consisting of SEQ ID NOs: 713-716, 718-734, 737-741, 743-744,746-765, 767-784, 786-788, 790-795, 797, 810-811, 813-876, 878-889,891-929, 931-1021, 1029-1064, 1067-1074, 1076-1080, 1082-1088,1091-1092, 1094-1153, 9283-9526, 9536, 9550-9772, 9825, 9832, 9843-9881,9899, 9908, 9925-9988, 9990-10284, 10290-11275, 11278-11279,11282-11284, 11289-11295, 11297-11299, 11301, 11303-11305, 11308-11312,11314, 11384, 11386, 11394, 11400, 11407, 11416-11417, 11421,11425-11426, 11429, 11433, 11439-11441, 11443-11444, 11446-11447,11449-11450, 11453-11455, 11457, 11460, 11468-11469, 11471, 11475,11482, 11485, 11488, 11494-11496, 11500-11503, 11505-11506, 11510-11513,11516-11525, 11530, 11551, 11555, 11559, 11561, 11570-11571, 11582,11589, 11605, 11612, 11695, 11697, 11699-13027, 13057, 13066,13091-13092, 13104, 13109, 13116, 13119-13180, 13188, 13192-13327,13329-13352, 13355-13929, 13941-13942, 13946-14913, 14989-15034,15037-15049, 15051-15072, 15074-15221, 15229-15252, 15254-15272,15281-15409, 15425, 15428-15434, and 15455-15722.

In some embodiments, the plant root stock transgenically expresses apolynucleotide encoding a polypeptide at least about 80%, at least about81%, at least about 82%, at least about 83%, at least about 84%, atleast about 85%, at least about 86%, at least about 87%, at least about88%, at least about 89%, at least about 90%, at least about 91%, atleast about 92%, at least about 93%, at least about 93%, at least about94%, at least about 95%, at least about 96%, at least about 97%, atleast about 98%, at least about 99%, e.g., 100% homologous (oridentical) to the amino acid sequence selected from the group consistingof SEQ ID NOs: 713-716, 718-734, 737-741, 743-744, 746-765, 767-784,786-788, 790-795, 797, 810-811, 813-876, 878-889, 891-929, 931-1021,1029-1064, 1067-1074, 1076-1080, 1082-1088, 1091-1092, 1094-1153,9283-9526, 9536, 9550-9772, 9825, 9832, 9843-9881, 9899, 9908,9925-9988, 9990-10284, 10290-11275, 11278-11279, 11282-11284,11289-11295, 11297-11299, 11301, 11303-11305, 11308-11312, 11314, 11384,11386, 11394, 11400, 11407, 11416-11417, 11421, 11425-11426, 11429,11433, 11439-11441, 11443-11444, 11446-11447, 11449-11450, 11453-11455,11457, 11460, 11468-11469, 11471, 11475, 11482, 11485, 11488,11494-11496, 11500-11503, 11505-11506, 11510-11513, 11516-11525, 11530,11551, 11555, 11559, 11561, 11570-11571, 11582, 11589, 11605, 11612,11695, 11697, 11699-13027, 13057, 13066, 13091-13092, 13104, 13109,13116, 13119-13180, 13188, 13192-13327, 13329-13352, 13355-13929,13941-13942, 13946-14913, 14989-15034, 15037-15049, 15051-15072,15074-15221, 15229-15252, 15254-15272, 15281-15409, 15425, 15428-15434,and 15455-15722 in a stress responsive manner.

According to some embodiments of the invention, the plant root stocktransgenically expresses a polynucleotide encoding a polypeptideselected from the group consisting of SEQ ID NOs: 713-735, 737-741,743-765, 767-795, 797, 809-1021, 1029-1064, 1067-1080, 1082-1092,1094-1153, 9276-9281, 9283-9532, 9534-9541, 9543-9545, 9548-9774, 9776,9778-9785, 9788-9791, 9793-9801, 9803, 9806-9807, 9809-9820, 9822-9823,9825-9838, 9840-9841, 9843-9881, 9889-9890, 9893-9894, 9897-9899, 9901,9904, 9906, 9908-9910, 9912-10285, 10287-11276, 11278-11319, 11321,11323, 11328-11330, 11333-11336, 11339-11342, 11344-11355, 11357,11359-11362, 11364-11366, 11369-13113, 13115-13944, 13946-14913, 14915,14917-14918, 14920-14921, 14923-14924, 14927-14933, 14937, 14939-14940,14942, 14944-14949, 14951, 14953, 14955-14958, 14960-14962, 14964-14971,14973, 14976, 14978-14979, 14989-15221, 15225-15272, 15275-15410,15412-15420, 15422-15423, 15425-15426, 15428-15434, 15436, 15440-15441,15443-15444, 15446, 15448-15449, and 15451-15726.

According to some embodiments of the invention, the plant root stocktransgenically expresses a polynucleotide comprising a nucleic acidsequence at least about 80%, at least about 81%, at least about 82%, atleast about 83%, at least about 84%, at least about 85%, at least about86%, at least about 87%, at least about 88%, at least about 89%, atleast about 90%, at least about 91%, at least about 92%, at least about93%, at least about 93%, at least about 94%, at least about 95%, atleast about 96%, at least about 97%, at least about 98%, at least about99%, e.g., 100% identical to the polynucleotide selected from the groupconsisting of SEQ ID NOs: 4-7, 9-25, 28-32, 34-35, 37-56, 58-75, 77-79,81-86, 88, 101-102, 104-167, 169-180, 182-220, 222-312, 320-389, 391,395-398, 400-416, 419-423, 425-426, 428-447, 449-464, 466-468, 470-475,477, 490-491, 493-555, 557-568, 570-605, 607-696, 704-709, 1164-1439,1453, 1468-1733, 1788, 1795, 1806-1860, 1884, 1899, 1917-2324,2331-3501, 3504-3506, 3509-3511, 3518-3526, 3528-3530, 3532, 3534-3536,3540-3547, 3549, 3638, 3641-3643, 3652, 3661, 3663, 3668, 3671,3683-3684, 3689, 3695-3696, 3700-3702, 3708, 3715-3718, 3720-3721,3723-3724, 3726-3727, 3732-3733, 3735, 3737, 3740, 3750-3751, 3753,3757, 3764-3765, 3768, 3772, 3776, 3783-3785, 3789-3792, 3794-3795,3800-3803, 3806-3818, 3827, 3889, 3894, 3898, 3900, 3915-3916, 3936,3943, 3964, 3971, 4099, 4101, 4103-4245, 4247-6064, 6103, 6112,6137-6138, 6150, 6155, 6162, 6165-6237, 6245, 6249-6406, 6408-6434,6437-7124, 7140-7141, 7145-8305, 8387-8453, 8457-8472, 8474-8505,8507-8683, 8691-8720, 8722-8748, 8757-8898, 8915, 8918-8927, and8948-9271.

According to some embodiments of the invention, the plant root stocktransgenically expresses a polynucleotide selected from the groupconsisting of SEQ ID NOs: 4-86, 88, 100-312, 320-389, 391, 395-475, 477,489-696, 704-709, 1157-4245, 4247-8375, 8387-8683, and 8686-9275.

Since processes which increase yield, seed yield, biomass, growth rate,vigor, oil content, fiber yield, fiber quality, fiber length,photosynthetic capacity, abiotic stress tolerance, and/or nitrogen useefficiency of a plant can involve multiple genes acting additively or insynergy (see, for example, in Quesda et al., Plant Physiol. 130:951-063,2002), the present invention also envisages expressing a plurality ofexogenous polynucleotides in a single host plant to thereby achievesuperior effect on nitrogen use efficiency, fertilizer use efficiency,oil content, yield, seed yield, fiber yield, fiber quality, fiberlength, photosynthetic capacity, growth rate, biomass, vigor and/orabiotic stress tolerance.

Expressing a plurality of exogenous polynucleotides in a single hostplant can be effected by co-introducing multiple nucleic acidconstructs, each including a different exogenous polynucleotide, into asingle plant cell. The transformed cell can then be regenerated into amature plant using the methods described hereinabove.

Alternatively, expressing a plurality of exogenous polynucleotides in asingle host plant can be effected by co-introducing into a singleplant-cell a single nucleic-acid construct including a plurality ofdifferent exogenous polynucleotides. Such a construct can be designedwith a single promoter sequence which can transcribe a polycistronicmessenger RNA including all the different exogenous polynucleotidesequences. To enable co-translation of the different polypeptidesencoded by the polycistronic messenger RNA, the polynucleotide sequencescan be inter-linked via an internal ribosome entry site (IRES) sequencewhich facilitates translation of polynucleotide sequences positioneddownstream of the IRES sequence. In this case, a transcribedpolycistronic RNA molecule encoding the different polypeptides describedabove will be translated from both the capped 5′ end and the twointernal IRES sequences of the polycistronic RNA molecule to therebyproduce in the cell all different polypeptides. Alternatively, theconstruct can include several promoter sequences each linked to adifferent exogenous polynucleotide sequence.

The plant cell transformed with the construct including a plurality ofdifferent exogenous polynucleotides, can be regenerated into a matureplant, using the methods described hereinabove.

Alternatively, expressing a plurality of exogenous polynucleotides in asingle host plant can be effected by introducing different nucleic acidconstructs, including different exogenous polynucleotides, into aplurality of plants. The regenerated transformed plants can then becross-bred and resultant progeny selected for superior abiotic stresstolerance, water use efficiency, fertilizer use efficiency, growth,biomass, yield and/or vigor traits, using conventional plant breedingtechniques.

According to some embodiments of the invention, the method furthercomprising growing the plant expressing the exogenous polynucleotideunder the abiotic stress.

Non-limiting examples of abiotic stress conditions include, salinity,osmotic stress, drought, water deprivation, excess of water (e.g.,flood, waterlogging), etiolation, low temperature (e.g., cold stress),high temperature, heavy metal toxicity, anaerobiosis, nutrientdeficiency (e.g., nitrogen deficiency or nitrogen limitation), nutrientexcess, atmospheric pollution and UV irradiation.

According to some embodiments of the invention, the method furthercomprising growing the plant expressing the exogenous polynucleotideunder fertilizer limiting conditions (e.g., nitrogen-limitingconditions). Non-limiting examples include growing the plant on soilswith low nitrogen content (40-50% Nitrogen of the content present undernormal or optimal conditions), or even under sever nitrogen deficiency(0-10% Nitrogen of the content present under normal or optimalconditions), wherein the normal or optimal conditions include about 6-15mM Nitrogen, e.g., 6-10 mM Nitrogen).

Thus, the invention encompasses plants exogenously expressing thepolynucleotide(s), the nucleic acid constructs and/or polypeptide(s) ofthe invention.

Once expressed within the plant cell or the entire plant, the level ofthe polypeptide encoded by the exogenous polynucleotide can bedetermined by methods well known in the art such as, activity assays,Western blots using antibodies capable of specifically binding thepolypeptide, Enzyme-Linked Immuno Sorbent Assay (ELISA),radio-immuno-assays (RIA), immunohistochemistry, immunocytochemistry,immunofluorescence and the like.

Methods of determining the level in the plant of the RNA transcribedfrom the exogenous polynucleotide are well known in the art and include,for example, Northern blot analysis, reverse transcription polymerasechain reaction (RT-PCR) analysis (including quantitative,semi-quantitative or real-time RT-PCR) and RNA-in situ hybridization.

The sequence information and annotations uncovered by the presentteachings can be harnessed in favor of classical breeding. Thus,sub-sequence data of those polynucleotides described above, can be usedas markers for marker assisted selection (MAS), in which a marker isused for indirect selection of a genetic determinant or determinants ofa trait of interest (e.g., biomass, growth rate, oil content, yield,abiotic stress tolerance, water use efficiency, nitrogen use efficiencyand/or fertilizer use efficiency). Nucleic acid data of the presentteachings (DNA or RNA sequence) may contain or be linked to polymorphicsites or genetic markers on the genome such as restriction fragmentlength polymorphism (RFLP), microsatellites and single nucleotidepolymorphism (SNP), DNA fingerprinting (DFP), amplified fragment lengthpolymorphism (AFLP), expression level polymorphism, polymorphism of theencoded polypeptide and any other polymorphism at the DNA or RNAsequence.

Examples of marker assisted selections include, but are not limited to,selection for a morphological trait (e.g., a gene that affects form,coloration, male sterility or resistance such as the presence or absenceof awn, leaf sheath coloration, height, grain color, aroma of rice);selection for a biochemical trait (e.g., a gene that encodes a proteinthat can be extracted and observed; for example, isozymes and storageproteins); selection for a biological trait (e.g., pathogen races orinsect biotypes based on host pathogen or host parasite interaction canbe used as a marker since the genetic constitution of an organism canaffect its susceptibility to pathogens or parasites).

The polynucleotides and polypeptides described hereinabove can be usedin a wide range of economical plants, in a safe and cost effectivemanner

Plant lines exogenously expressing the polynucleotide or the polypeptideof the invention are screened to identify those that show the greatestincrease of the desired plant trait.

Thus, according to an additional embodiment of the present invention,there is provided a method of evaluating a trait of a plant, the methodcomprising: (a) expressing in a plant or a portion thereof the nucleicacid construct of some embodiments of the invention; and (b) evaluatinga trait of a plant as compared to a wild type plant of the same type(e.g., a plant not transformed with the claimed biomolecules); therebyevaluating the trait of the plant.

According to an aspect of some embodiments of the invention there isprovided a method of producing a crop comprising growing a crop of aplant expressing an exogenous polynucleotide comprising a nucleic acidsequence encoding a polypeptide at least about 80%, at least about 81%,at least about 82%, at least about 83%, at least about 84%, at leastabout 85%, at least about 86%, at least about 87%, at least about 88%,at least about 89%, at least about 90%, at least about 91%, at leastabout 92%, at least about 93%, at least about 94%, at least about 95%,at least about 96%, at least about 97%, at least about 98%, at leastabout 99%, or more say 100% homologous (e.g., identical) to the aminoacid sequence selected from the group consisting of SEQ ID NOs: 713-716,718-734, 737-741, 743-744, 746-765, 767-784, 786-788, 790-795, 797,810-811, 813-876, 878-889, 891-929, 931-1021, 1029-1064, 1067-1074,1076-1080, 1082-1088, 1091-1092, 1094-1153, 9283-9526, 9536, 9550-9772,9825, 9832, 9843-9881, 9899, 9908, 9925-9988, 9990-10284, 10290-11275,11278-11279, 11282-11284, 11289-11295, 11297-11299, 11301, 11303-11305,11308-11312, 11314, 11384, 11386, 11394, 11400, 11407, 11416-11417,11421, 11425-11426, 11429, 11433, 11439-11441, 11443-11444, 11446-11447,11449-11450, 11453-11455, 11457, 11460, 11468-11469, 11471, 11475,11482, 11485, 11488, 11494-11496, 11500-11503, 11505-11506, 11510-11513,11516-11525, 11530, 11551, 11555, 11559, 11561, 11570-11571, 11582,11589, 11605, 11612, 11695, 11697, 11699-13027, 13057, 13066,13091-13092, 13104, 13109, 13116, 13119-13180, 13188, 13192-13327,13329-13352, 13355-13929, 13941-13942, 13946-14913, 14989-15034,15037-15049, 15051-15072, 15074-15221, 15229-15252, 15254-15272,15281-15409, 15425, 15428-15434, and 15455-15722, wherein the plant isderived from a plant (parent plant) that has been transformed to expressthe exogenous polynucleotide and that has been selected for increasedabiotic stress tolerance, increased water use efficiency, increasedgrowth rate, increased vigor, increased biomass, increased oil content,increased yield, increased seed yield, increased fiber yield, increasedfiber quality, increased fiber length, increased photosyntheticcapacity, and/or increased fertilizer use efficiency (e.g., increasednitrogen use efficiency) as compared to a control plant, therebyproducing the crop.

According to an aspect of some embodiments of the present inventionthere is provided a method of producing a crop comprising growing a cropplant transformed with an exogenous polynucleotide encoding apolypeptide at least 80%, at least about 81%, at least about 82%, atleast about 83%, at least about 84%, at least about 85%, at least about86%, at least about 87%, at least about 88%, at least about 89%, atleast about 90%, at least about 91%, at least about 92%, at least about93%, at least about 94%, at least about 95%, at least about 96%, atleast about 97%, at least about 98%, at least about 99%, or more say100% homologous (e.g., identical) to the amino acid sequence selectedfrom the group consisting of SEQ ID NOs: 713-716, 718-734, 737-741,743-744, 746-765, 767-784, 786-788, 790-795, 797, 810-811, 813-876,878-889, 891-929, 931-1021, 1029-1064, 1067-1074, 1076-1080, 1082-1088,1091-1092, 1094-1153, 9283-9526, 9536, 9550-9772, 9825, 9832, 9843-9881,9899, 9908, 9925-9988, 9990-10284, 10290-11275, 11278-11279,11282-11284, 11289-11295, 11297-11299, 11301, 11303-11305, 11308-11312,11314, 11384, 11386, 11394, 11400, 11407, 11416-11417, 11421,11425-11426, 11429, 11433, 11439-11441, 11443-11444, 11446-11447,11449-11450, 11453-11455, 11457, 11460, 11468-11469, 11471, 11475,11482, 11485, 11488, 11494-11496, 11500-11503, 11505-11506, 11510-11513,11516-11525, 11530, 11551, 11555, 11559, 11561, 11570-11571, 11582,11589, 11605, 11612, 11695, 11697, 11699-13027, 13057, 13066,13091-13092, 13104, 13109, 13116, 13119-13180, 13188, 13192-13327,13329-13352, 13355-13929, 13941-13942, 13946-14913, 14989-15034,15037-15049, 15051-15072, 15074-15221, 15229-15252, 15254-15272,15281-15409, 15425, 15428-15434, and 15455-15722, wherein the crop plantis derived from plants which have been transformed with the exogenouspolynucleotide and which have been selected for increased abiotic stresstolerance, increased water use efficiency, increased growth rate,increased vigor, increased biomass, increased oil content, increasedyield, increased seed yield, increased fiber yield, increased fiberquality, increased fiber length, increased photosynthetic capacity,and/or increased fertilizer use efficiency (e.g., increased nitrogen useefficiency) as compared to a wild type plant of the same species whichis grown under the same growth conditions, and the crop plant having theincreased abiotic stress tolerance, increased water use efficiency,increased growth rate, increased vigor, increased biomass, increased oilcontent, increased yield, increased seed yield, increased fiber yield,increased fiber quality, increased fiber length, increasedphotosynthetic capacity, and/or increased fertilizer use efficiency(e.g., increased nitrogen use efficiency), thereby producing the crop.

According to some embodiments of the invention the polypeptide isselected from the group consisting of SEQ ID NOs: 713-735, 737-741,743-765, 767-795, 797, 809-1021, 1029-1064, 1067-1080, 1082-1092,1094-1153, 9276-9281, 9283-9532, 9534-9541, 9543-9545, 9548-9774, 9776,9778-9785, 9788-9791, 9793-9801, 9803, 9806-9807, 9809-9820, 9822-9823,9825-9838, 9840-9841, 9843-9881, 9889-9890, 9893-9894, 9897-9899, 9901,9904, 9906, 9908-9910, 9912-10285, 10287-11276, 11278-11319, 11321,11323, 11328-11330, 11333-11336, 11339-11342, 11344-11355, 11357,11359-11362, 11364-11366, 11369-13113, 13115-13944, 13946-14913, 14915,14917-14918, 14920-14921, 14923-14924, 14927-14933, 14937, 14939-14940,14942, 14944-14949, 14951, 14953, 14955-14958, 14960-14962, 14964-14971,14973, 14976, 14978-14979, 14989-15221, 15225-15272, 15275-15410,15412-15420, 15422-15423, 15425-15426, 15428-15434, 15436, 15440-15441,15443-15444, 15446, 15448-15449, and 15451-15726.

According to an aspect of some embodiments of the invention there isprovided a method of producing a crop comprising growing a crop of aplant expressing an exogenous polynucleotide which comprises a nucleicacid sequence which is at least about 80%, at least about 81%, at leastabout 82%, at least about 83%, at least about 84%, at least about 85%,at least about 86%, at least about 87%, at least about 88%, at leastabout 89%, at least about 90%, at least about 91%, at least about 92%,at least about 93%, at least about 93%, at least about 94%, at leastabout 95%, at least about 96%, at least about 97%, at least about 98%,at least about 99%, e.g., 100% identical to the nucleic acid sequenceselected from the group consisting of SEQ ID NOs: 4-7, 9-25, 28-32,34-35, 37-56, 58-75, 77-79, 81-86, 88, 101-102, 104-167, 169-180,182-220, 222-312, 320-389, 391, 395-398, 400-416, 419-423, 425-426,428-447, 449-464, 466-468, 470-475, 477, 490-491, 493-555, 557-568,570-605, 607-696, 704-709, 1164-1439, 1453, 1468-1733, 1788, 1795,1806-1860, 1884, 1899, 1917-2324, 2331-3501, 3504-3506, 3509-3511,3518-3526, 3528-3530, 3532, 3534-3536, 3540-3547, 3549, 3638, 3641-3643,3652, 3661, 3663, 3668, 3671, 3683-3684, 3689, 3695-3696, 3700-3702,3708, 3715-3718, 3720-3721, 3723-3724, 3726-3727, 3732-3733, 3735, 3737,3740, 3750-3751, 3753, 3757, 3764-3765, 3768, 3772, 3776, 3783-3785,3789-3792, 3794-3795, 3800-3803, 3806-3818, 3827, 3889, 3894, 3898,3900, 3915-3916, 3936, 3943, 3964, 3971, 4099, 4101, 4103-4245,4247-6064, 6103, 6112, 6137-6138, 6150, 6155, 6162, 6165-6237, 6245,6249-6406, 6408-6434, 6437-7124, 7140-7141, 7145-8305, 8387-8453,8457-8472, 8474-8505, 8507-8683, 8691-8720, 8722-8748, 8757-8898, 8915,8918-8927, and 8948-9271, wherein the plant is derived from a plantselected for increased abiotic stress tolerance, increased water useefficiency, increased growth rate, increased vigor, increased biomass,increased oil content, increased yield, increased seed yield, increasedfiber yield, increased fiber quality, increased fiber length, increasedphotosynthetic capacity, and/or increased fertilizer use efficiency(e.g., increased nitrogen use efficiency) as compared to a controlplant, thereby producing the crop.

According to an aspect of some embodiments of the present inventionthere is provided a method of producing a crop comprising growing a cropplant transformed with an exogenous polynucleotide at least 80%, atleast about 81%, at least about 82%, at least about 83%, at least about84%, at least about 85%, at least about 86%, at least about 87%, atleast about 88%, at least about 89%, at least about 90%, at least about91%, at least about 92%, at least about 93%, at least about 94%, atleast about 95%, at least about 96%, at least about 97%, at least about98%, at least about 99%, or more say 100% identical to the nucleic acidsequence selected from the group consisting of SEQ ID NOs: 4-7, 9-25,28-32, 34-35, 37-56, 58-75, 77-79, 81-86, 88, 101-102, 104-167, 169-180,182-220, 222-312, 320-389, 391, 395-398, 400-416, 419-423, 425-426,428-447, 449-464, 466-468, 470-475, 477, 490-491, 493-555, 557-568,570-605, 607-696, 704-709, 1164-1439, 1453, 1468-1733, 1788, 1795,1806-1860, 1884, 1899, 1917-2324, 2331-3501, 3504-3506, 3509-3511,3518-3526, 3528-3530, 3532, 3534-3536, 3540-3547, 3549, 3638, 3641-3643,3652, 3661, 3663, 3668, 3671, 3683-3684, 3689, 3695-3696, 3700-3702,3708, 3715-3718, 3720-3721, 3723-3724, 3726-3727, 3732-3733, 3735, 3737,3740, 3750-3751, 3753, 3757, 3764-3765, 3768, 3772, 3776, 3783-3785,3789-3792, 3794-3795, 3800-3803, 3806-3818, 3827, 3889, 3894, 3898,3900, 3915-3916, 3936, 3943, 3964, 3971, 4099, 4101, 4103-4245,4247-6064, 6103, 6112, 6137-6138, 6150, 6155, 6162, 6165-6237, 6245,6249-6406, 6408-6434, 6437-7124, 7140-7141, 7145-8305, 8387-8453,8457-8472, 8474-8505, 8507-8683, 8691-8720, 8722-8748, 8757-8898, 8915,8918-8927, and 8948-9271, wherein the crop plant is derived from plantswhich have been transformed with the exogenous polynucleotide and whichhave been selected for increased abiotic stress tolerance, increasedwater use efficiency, increased growth rate, increased vigor, increasedbiomass, increased oil content, increased yield, increased seed yield,increased fiber yield, increased fiber quality, increased fiber length,increased photosynthetic capacity, and/or increased fertilizer useefficiency (e.g., increased nitrogen use efficiency) as compared to awild type plant of the same species which is grown under the same growthconditions, and the crop plant having the increased abiotic stresstolerance, increased water use efficiency, increased growth rate,increased vigor, increased biomass, increased oil content, increasedyield, increased seed yield, increased fiber yield, increased fiberquality, increased fiber length, increased photosynthetic capacity,and/or increased fertilizer use efficiency (e.g., increased nitrogen useefficiency), thereby producing the crop.

According to some embodiments of the invention the exogenouspolynucleotide is selected from the group consisting of SEQ ID NOs:4-86, 88, 100-312, 320-389, 391, 395-475, 477, 489-696, 704-709,1157-4245, 4247-8375, 8387-8683, and 8686-9275.

According to an aspect of some embodiments of the invention there isprovided a method of growing a crop comprising seeding seeds and/orplanting plantlets of a plant transformed with the exogenouspolynucleotide of the invention, e.g., the polynucleotide which encodesthe polypeptide of some embodiments of the invention, wherein the plantis derived from plants which have been transformed with the exogenouspolynucleotide and which have been selected for at least one traitselected from the group consisting of increased abiotic stresstolerance, increased water use efficiency, increased growth rate,increased vigor, increased biomass, increased oil content, increasedyield, increased seed yield, increased fiber yield, increased fiberquality, increased fiber length, increased photosynthetic capacity,and/or increased fertilizer use efficiency (e.g., increased nitrogen useefficiency) as compared to a non-transformed plant.

According to some embodiments of the invention the method of growing acrop comprising seeding seeds and/or planting plantlets of a planttransformed with an exogenous polynucleotide comprising a nucleic acidsequence encoding a polypeptide at least about 80%, at least about 81%,at least about 82%, at least about 83%, at least about 84%, at leastabout 85%, at least about 86%, at least about 87%, at least about 88%,at least about 89%, at least about 90%, at least about 91%, at leastabout 92%, at least about 93%, at least about 93%, at least about 94%,at least about 95%, at least about 96%, at least about 97%, at leastabout 98%, at least about 99%, e.g., 100% identical to SEQ ID NO:713-716, 718-734, 737-741, 743-744, 746-765, 767-784, 786-788, 790-795,797, 810-811, 813-876, 878-889, 891-929, 931-1021, 1029-1064, 1067-1074,1076-1080, 1082-1088, 1091-1092, 1094-1153, 9283-9526, 9536, 9550-9772,9825, 9832, 9843-9881, 9899, 9908, 9925-9988, 9990-10284, 10290-11275,11278-11279, 11282-11284, 11289-11295, 11297-11299, 11301, 11303-11305,11308-11312, 11314, 11384, 11386, 11394, 11400, 11407, 11416-11417,11421, 11425-11426, 11429, 11433, 11439-11441, 11443-11444, 11446-11447,11449-11450, 11453-11455, 11457, 11460, 11468-11469, 11471, 11475,11482, 11485, 11488, 11494-11496, 11500-11503, 11505-11506, 11510-11513,11516-11525, 11530, 11551, 11555, 11559, 11561, 11570-11571, 11582,11589, 11605, 11612, 11695, 11697, 11699-13027, 13057, 13066,13091-13092, 13104, 13109, 13116, 13119-13180, 13188, 13192-13327,13329-13352, 13355-13929, 13941-13942, 13946-14913, 14989-15034,15037-15049, 15051-15072, 15074-15221, 15229-15252, 15254-15272,15281-15409, 15425, 15428-15434, 15455-15721 or 15722, wherein the plantis derived from plants which have been transformed with the exogenouspolynucleotide and which have been selected for at least one traitselected from the group consisting of increased abiotic stresstolerance, increased water use efficiency, increased growth rate,increased vigor, increased biomass, increased oil content, increasedyield, increased seed yield, increased fiber yield, increased fiberquality, increased fiber length, increased photosynthetic capacity,and/or increased fertilizer use efficiency (e.g., increased nitrogen useefficiency) as compared to a non-transformed plant, thereby growing thecrop.

According to some embodiments of the invention the polypeptide isselected from the group consisting of SEQ ID NOs: 713-735, 737-741,743-765, 767-795, 797, 809-1021, 1029-1064, 1067-1080, 1082-1092,1094-1153, 9276-9281, 9283-9532, 9534-9541, 9543-9545, 9548-9774, 9776,9778-9785, 9788-9791, 9793-9801, 9803, 9806-9807, 9809-9820, 9822-9823,9825-9838, 9840-9841, 9843-9881, 9889-9890, 9893-9894, 9897-9899, 9901,9904, 9906, 9908-9910, 9912-10285, 10287-11276, 11278-11319, 11321,11323, 11328-11330, 11333-11336, 11339-11342, 11344-11355, 11357,11359-11362, 11364-11366, 11369-13113, 13115-13944, 13946-14913, 14915,14917-14918, 14920-14921, 14923-14924, 14927-14933, 14937, 14939-14940,14942, 14944-14949, 14951, 14953, 14955-14958, 14960-14962, 14964-14971,14973, 14976, 14978-14979, 14989-15221, 15225-15272, 15275-15410,15412-15420, 15422-15423, 15425-15426, 15428-15434, 15436, 15440-15441,15443-15444, 15446, 15448-15449, and 15451-15726.

According to some embodiments of the invention the method of growing acrop comprising seeding seeds and/or planting plantlets of a planttransformed with an exogenous polynucleotide comprising the nucleic acidsequence at least about 80%, at least about 81%, at least about 82%, atleast about 83%, at least about 84%, at least about 85%, at least about86%, at least about 87%, at least about 88%, at least about 89%, atleast about 90%, at least about 91%, at least about 92%, at least about93%, at least about 93%, at least about 94%, at least about 95%, atleast about 96%, at least about 97%, at least about 98%, at least about99%, e.g., 100% identical to SEQ ID NO: 4-7, 9-25, 28-32, 34-35, 37-56,58-75, 77-79, 81-86, 88, 101-102, 104-167, 169-180, 182-220, 222-312,320-389, 391, 395-398, 400-416, 419-423, 425-426, 428-447, 449-464,466-468, 470-475, 477, 490-491, 493-555, 557-568, 570-605, 607-696,704-709, 1164-1439, 1453, 1468-1733, 1788, 1795, 1806-1860, 1884, 1899,1917-2324, 2331-3501, 3504-3506, 3509-3511, 3518-3526, 3528-3530, 3532,3534-3536, 3540-3547, 3549, 3638, 3641-3643, 3652, 3661, 3663, 3668,3671, 3683-3684, 3689, 3695-3696, 3700-3702, 3708, 3715-3718, 3720-3721,3723-3724, 3726-3727, 3732-3733, 3735, 3737, 3740, 3750-3751, 3753,3757, 3764-3765, 3768, 3772, 3776, 3783-3785, 3789-3792, 3794-3795,3800-3803, 3806-3818, 3827, 3889, 3894, 3898, 3900, 3915-3916, 3936,3943, 3964, 3971, 4099, 4101, 4103-4245, 4247-6064, 6103, 6112,6137-6138, 6150, 6155, 6162, 6165-6237, 6245, 6249-6406, 6408-6434,6437-7124, 7140-7141, 7145-8305, 8387-8453, 8457-8472, 8474-8505,8507-8683, 8691-8720, 8722-8748, 8757-8898, 8915, 8918-8927, 8948-9270or 9271, wherein the plant is derived from plants which have beentransformed with the exogenous polynucleotide and which have beenselected for at least one trait selected from the group consisting ofincreased abiotic stress tolerance, increased water use efficiency,increased growth rate, increased vigor, increased biomass, increased oilcontent, increased yield, increased seed yield, increased fiber yield,increased fiber quality, increased fiber length, increasedphotosynthetic capacity, and/or increased fertilizer use efficiency(e.g., increased nitrogen use efficiency) as compared to anon-transformed plant, thereby growing the crop.

According to some embodiments of the invention the exogenouspolynucleotide is selected from the group consisting of SEQ ID NOs:4-86, 88, 100-312, 320-389, 391, 395-475, 477, 489-696, 704-709,1157-4245, 4247-8375, 8387-8683, and 8686-9275.

According to an aspect of some embodiments of the present inventionthere is provided a method of growing a crop comprising:

(a) selecting a parent plant transformed with an exogenouspolynucleotide comprising a nucleic acid sequence encoding a polypeptideat least about 80%, at least about 81%, at least about 82%, at leastabout 83%, at least about 84%, at least about 85%, at least about 86%,at least about 87%, at least about 88%, at least about 89%, at leastabout 90%, at least about 91%, at least about 92%, at least about 93%,at least about 93%, at least about 94%, at least about 95%, at leastabout 96%, at least about 97%, at least about 98%, at least about 99%,e.g., 100% identical to the polypeptide selected from the groupconsisting of set forth in SEQ ID NOs: 713-716, 718-734, 737-741,743-744, 746-765, 767-784, 786-788, 790-795, 797, 810-811, 813-876,878-889, 891-929, 931-1021, 1029-1064, 1067-1074, 1076-1080, 1082-1088,1091-1092, 1094-1153, 9283-9526, 9536, 9550-9772, 9825, 9832, 9843-9881,9899, 9908, 9925-9988, 9990-10284, 10290-11275, 11278-11279,11282-11284, 11289-11295, 11297-11299, 11301, 11303-11305, 11308-11312,11314, 11384, 11386, 11394, 11400, 11407, 11416-11417, 11421,11425-11426, 11429, 11433, 11439-11441, 11443-11444, 11446-11447,11449-11450, 11453-11455, 11457, 11460, 11468-11469, 11471, 11475,11482, 11485, 11488, 11494-11496, 11500-11503, 11505-11506, 11510-11513,11516-11525, 11530, 11551, 11555, 11559, 11561, 11570-11571, 11582,11589, 11605, 11612, 11695, 11697, 11699-13027, 13057, 13066,13091-13092, 13104, 13109, 13116, 13119-13180, 13188, 13192-13327,13329-13352, 13355-13929, 13941-13942, 13946-14913, 14989-15034,15037-15049, 15051-15072, 15074-15221, 15229-15252, 15254-15272,15281-15409, 15425, 15428-15434, and 15455-15722 for at least one traitselected from the group consisting of: increased yield, increased growthrate, increased biomass, increased vigor, increased oil content,increased seed yield, increased fiber yield, increased fiber quality,increased fiber length, increased photosynthetic capacity, increasednitrogen use efficiency, and increased abiotic stress tolerance ascompared to a non-transformed plant of the same species which is grownunder the same growth conditions, and

(b) growing progeny crop plant of said parent plant, wherein saidprogeny crop plant which comprises said exogenous polynucleotide hassaid increased yield, said increased growth rate, said increasedbiomass, said increased vigor, said increased oil content, saidincreased seed yield, said increased fiber yield, said increased fiberquality, said increased fiber length, said increased photosyntheticcapacity, said increased nitrogen use efficiency, and/or said increasedabiotic stress, thereby growing the crop.

According to an aspect of some embodiments of the present inventionthere is provided a method of producing seeds of a crop comprising:

(a) selecting parent plant transformed with an exogenous polynucleotidecomprising a nucleic acid sequence encoding a polypeptide at least about80%, at least about 81%, at least about 82%, at least about 83%, atleast about 84%, at least about 85%, at least about 86%, at least about87%, at least about 88%, at least about 89%, at least about 90%, atleast about 91%, at least about 92%, at least about 93%, at least about93%, at least about 94%, at least about 95%, at least about 96%, atleast about 97%, at least about 98%, at least about 99%, e.g., 100%identical to the polypeptide selected from the group consisting of setforth in SEQ ID NOs: 713-716, 718-734, 737-741, 743-744, 746-765,767-784, 786-788, 790-795, 797, 810-811, 813-876, 878-889, 891-929,931-1021, 1029-1064, 1067-1074, 1076-1080, 1082-1088, 1091-1092,1094-1153, 9283-9526, 9536, 9550-9772, 9825, 9832, 9843-9881, 9899,9908, 9925-9988, 9990-10284, 10290-11275, 11278-11279, 11282-11284,11289-11295, 11297-11299, 11301, 11303-11305, 11308-11312, 11314, 11384,11386, 11394, 11400, 11407, 11416-11417, 11421, 11425-11426, 11429,11433, 11439-11441, 11443-11444, 11446-11447, 11449-11450, 11453-11455,11457, 11460, 11468-11469, 11471, 11475, 11482, 11485, 11488,11494-11496, 11500-11503, 11505-11506, 11510-11513, 11516-11525, 11530,11551, 11555, 11559, 11561, 11570-11571, 11582, 11589, 11605, 11612,11695, 11697, 11699-13027, 13057, 13066, 13091-13092, 13104, 13109,13116, 13119-13180, 13188, 13192-13327, 13329-13352, 13355-13929,13941-13942, 13946-14913, 14989-15034, 15037-15049, 15051-15072,15074-15221, 15229-15252, 15254-15272, 15281-15409, 15425, 15428-15434,and 15455-15722 for at least one trait selected from the groupconsisting of: increased yield, increased growth rate, increasedbiomass, increased vigor, increased oil content, increased seed yield,increased fiber yield, increased fiber quality, increased fiber length,increased photosynthetic capacity, increased nitrogen use efficiency,and increased abiotic stress as compared to a non-transformed plant ofthe same species which is grown under the same growth conditions,

(b) growing a seed producing plant from said parent plant resultant ofstep (a), wherein said seed producing plant which comprises saidexogenous polynucleotide having said increased yield, said increasedgrowth rate, said increased biomass, said increased vigor, saidincreased oil content, said increased seed yield, said increased fiberyield, said increased fiber quality, said increased fiber length, saidincreased photosynthetic capacity, said increased nitrogen useefficiency, and/or said increased abiotic stress, and

(c) producing seeds from said seed producing plant resultant of step(b), thereby producing seeds of the crop.

According to an aspect of some embodiments of the present inventionthere is provided a method of growing a crop comprising:

(a) selecting a parent plant transformed with an exogenouspolynucleotide comprising a nucleic acid sequence encoding thepolypeptide selected from the group consisting of set forth in SEQ IDNOs: 713-735, 737-741, 743-765, 767-795, 797, 809-1021, 1029-1064,1067-1080, 1082-1092, 1094-1153, 9276-9281, 9283-9532, 9534-9541,9543-9545, 9548-9774, 9776, 9778-9785, 9788-9791, 9793-9801, 9803,9806-9807, 9809-9820, 9822-9823, 9825-9838, 9840-9841, 9843-9881,9889-9890, 9893-9894, 9897-9899, 9901, 9904, 9906, 9908-9910,9912-10285, 10287-11276, 11278-11319, 11321, 11323, 11328-11330,11333-11336, 11339-11342, 11344-11355, 11357, 11359-11362, 11364-11366,11369-13113, 13115-13944, 13946-14913, 14915, 14917-14918, 14920-14921,14923-14924, 14927-14933, 14937, 14939-14940, 14942, 14944-14949, 14951,14953, 14955-14958, 14960-14962, 14964-14971, 14973, 14976, 14978-14979,14989-15221, 15225-15272, 15275-15410, 15412-15420, 15422-15423,15425-15426, 15428-15434, 15436, 15440-15441, 15443-15444, 15446,15448-15449, and 15451-15726 for at least one trait selected from thegroup consisting of: increased yield, increased growth rate, increasedbiomass, increased vigor, increased oil content, increased seed yield,increased fiber yield, increased fiber quality, increased fiber length,increased photosynthetic capacity, increased nitrogen use efficiency,and increased abiotic stress tolerance as compared to a non-transformedplant of the same species which is grown under the same growthconditions, and

(b) growing progeny crop plant of said parent plant, wherein saidprogeny crop plant which comprises said exogenous polynucleotide hassaid increased yield, said increased growth rate, said increasedbiomass, said increased vigor, said increased oil content, saidincreased seed yield, said increased fiber yield, said increased fiberquality, said increased fiber length, said increased photosyntheticcapacity, said increased nitrogen use efficiency, and/or said increasedabiotic stress, thereby growing the crop.

According to an aspect of some embodiments of the present inventionthere is provided a method of producing seeds of a crop comprising:

(a) selecting parent plant transformed with an exogenous polynucleotidecomprising a nucleic acid sequence encoding the polypeptide selectedfrom the group consisting of set forth in SEQ ID NOs: 713-735, 737-741,743-765, 767-795, 797, 809-1021, 1029-1064, 1067-1080, 1082-1092,1094-1153, 9276-9281, 9283-9532, 9534-9541, 9543-9545, 9548-9774, 9776,9778-9785, 9788-9791, 9793-9801, 9803, 9806-9807, 9809-9820, 9822-9823,9825-9838, 9840-9841, 9843-9881, 9889-9890, 9893-9894, 9897-9899, 9901,9904, 9906, 9908-9910, 9912-10285, 10287-11276, 11278-11319, 11321,11323, 11328-11330, 11333-11336, 11339-11342, 11344-11355, 11357,11359-11362, 11364-11366, 11369-13113, 13115-13944, 13946-14913, 14915,14917-14918, 14920-14921, 14923-14924, 14927-14933, 14937, 14939-14940,14942, 14944-14949, 14951, 14953, 14955-14958, 14960-14962, 14964-14971,14973, 14976, 14978-14979, 14989-15221, 15225-15272, 15275-15410,15412-15420, 15422-15423, 15425-15426, 15428-15434, 15436, 15440-15441,15443-15444, 15446, 15448-15449, and 15451-15726 for at least one traitselected from the group consisting of: increased yield, increased growthrate, increased biomass, increased vigor, increased oil content,increased seed yield, increased fiber yield, increased fiber quality,increased fiber length, increased photosynthetic capacity, increasednitrogen use efficiency, and increased abiotic stress as compared to anon-transformed plant of the same species which is grown under the samegrowth conditions,

(b) growing a seed producing plant from said parent plant resultant ofstep (a), wherein said seed producing plant which comprises saidexogenous polynucleotide having said increased yield, said increasedgrowth rate, said increased biomass, said increased vigor, saidincreased oil content, said increased seed yield, said increased fiberyield, said increased fiber quality, said increased fiber length, saidincreased photosynthetic capacity, said increased nitrogen useefficiency, and/or said increased abiotic stress, and

(c) producing seeds from said seed producing plant resultant of step(b), thereby producing seeds of the crop.

According to some embodiments of the invention the exogenouspolynucleotide is selected from the group consisting of SEQ ID NOs:4-86, 88, 100-312, 320-389, 391, 395-475, 477, 489-696, 704-709,1157-4245, 4247-8375, 8387-8683, and 8686-9275.

According to a specific embodiment of the invention, the exogenouspolynucleotide is not an homologue of the polynucleotide selected fromthe group consisting of: SEQ ID NOs: 3560, 3569, 3606, 3608, 8329, 8331,8351, 8360, 8688, 8939, 8947 and 9275.

According to a specific embodiment of the invention, the exogenouspolynucleotide does not encode a homologue of the polypeptide selectedfrom the group consisting of: SEQ ID NOs: 11323, 11330, 11364, 11366,14937, 14939, 14958, 14967, 15226, 15446, 15454, and 15726.

The effect of the transgene (the exogenous polynucleotide encoding thepolypeptide) on abiotic stress tolerance can be determined using knownmethods such as detailed below and in the Examples section whichfollows.

Abiotic stress tolerance—Transformed (i.e., expressing the transgene)and non-transformed (wild type) plants are exposed to an abiotic stresscondition, such as water deprivation, suboptimal temperature (lowtemperature, high temperature), nutrient deficiency, nutrient excess, asalt stress condition, osmotic stress, heavy metal toxicity,anaerobiosis, atmospheric pollution and UV irradiation.

Salinity tolerance assay—Transgenic plants with tolerance to high saltconcentrations are expected to exhibit better germination, seedlingvigor or growth in high salt. Salt stress can be effected in many wayssuch as, for example, by irrigating the plants with a hyperosmoticsolution, by cultivating the plants hydroponically in a hyperosmoticgrowth solution (e.g., Hoagland solution), or by culturing the plants ina hyperosmotic growth medium [e.g., 50% Murashige-Skoog medium (MSmedium)]. Since different plants vary considerably in their tolerance tosalinity, the salt concentration in the irrigation water, growthsolution, or growth medium can be adjusted according to the specificcharacteristics of the specific plant cultivar or variety, so as toinflict a mild or moderate effect on the physiology and/or morphology ofthe plants (for guidelines as to appropriate concentration see,Bernstein and Kafkafi, Root Growth Under Salinity Stress In: PlantRoots, The Hidden Half 3rd ed. Waisel Y, Eshel A and Kafkafi U.(editors) Marcel Dekker Inc., New York, 2002, and reference therein).

For example, a salinity tolerance test can be performed by irrigatingplants at different developmental stages with increasing concentrationsof sodium chloride (for example 50 mM, 100 mM, 200 mM, 400 mM NaCl)applied from the bottom and from above to ensure even dispersal of salt.Following exposure to the stress condition the plants are frequentlymonitored until substantial physiological and/or morphological effectsappear in wild type plants. Thus, the external phenotypic appearance,degree of wilting and overall success to reach maturity and yieldprogeny are compared between control and transgenic plants.

Quantitative parameters of tolerance measured include, but are notlimited to, the average wet and dry weight, growth rate, leaf size, leafcoverage (overall leaf area), the weight of the seeds yielded, theaverage seed size and the number of seeds produced per plant.Transformed plants not exhibiting substantial physiological and/ormorphological effects, or exhibiting higher biomass than wild-typeplants, are identified as abiotic stress tolerant plants.

Osmotic tolerance test—Osmotic stress assays (including sodium chlorideand mannitol assays) are conducted to determine if an osmotic stressphenotype was sodium chloride-specific or if it was a general osmoticstress related phenotype. Plants which are tolerant to osmotic stressmay have more tolerance to drought and/or freezing. For salt and osmoticstress germination experiments, the medium is supplemented for examplewith 50 mM, 100 mM, 200 mM NaCl or 100 mM, 200 mM NaCl, 400 mM mannitol.

Drought tolerance assay/Osmoticum assay—Tolerance to drought isperformed to identify the genes conferring better plant survival afteracute water deprivation. To analyze whether the transgenic plants aremore tolerant to drought, an osmotic stress produced by the non-ionicosmolyte sorbitol in the medium can be performed. Control and transgenicplants are germinated and grown in plant-agar plates for 4 days, afterwhich they are transferred to plates containing 500 mM sorbitol. Thetreatment causes growth retardation, then both control and transgenicplants are compared, by measuring plant weight (wet and dry), yield, andby growth rates measured as time to flowering.

Conversely, soil-based drought screens are performed with plantsoverexpressing the polynucleotides detailed above. Seeds from controlArabidopsis plants, or other transgenic plants overexpressing thepolypeptide of the invention are germinated and transferred to pots.Drought stress is obtained after irrigation is ceased accompanied byplacing the pots on absorbent paper to enhance the soil-drying rate.Transgenic and control plants are compared to each other when themajority of the control plants develop severe wilting. Plants arere-watered after obtaining a significant fraction of the control plantsdisplaying a severe wilting. Plants are ranked comparing to controls foreach of two criteria: tolerance to the drought conditions and recovery(survival) following re-watering.

Cold stress tolerance—To analyze cold stress, mature (25 day old) plantsare transferred to 4° C. chambers for 1 or 2 weeks, with constitutivelight. Later on plants are moved back to greenhouse. Two weeks laterdamages from chilling period, resulting in growth retardation and otherphenotypes, are compared between both control and transgenic plants, bymeasuring plant weight (wet and dry), and by comparing growth ratesmeasured as time to flowering, plant size, yield, and the like.

Heat stress tolerance—Heat stress tolerance is achieved by exposing theplants to temperatures above 34° C. for a certain period. Planttolerance is examined after transferring the plants back to 22° C. forrecovery and evaluation after 5 days relative to internal controls(non-transgenic plants) or plants not exposed to neither cold or heatstress.

Water Use Efficiency—can be determined as the biomass produced per unittranspiration. To analyze WUE, leaf relative water content can bemeasured in control and transgenic plants. Fresh weight (FW) isimmediately recorded; then leaves are soaked for 8 hours in distilledwater at room temperature in the dark, and the turgid weight (TW) isrecorded. Total dry weight (DW) is recorded after drying the leaves at60° C. to a constant weight. Relative water content (RWC) is calculatedaccording to the following Formula I:

Formula I

RWC=[(FW−DW)/(TW−DW)]×100

Fertilizer use efficiency—To analyze whether the transgenic plants aremore responsive to fertilizers, plants are grown in agar plates or potswith a limited amount of fertilizer, as described, for example, inYanagisawa et al (Proc Natl Acad Sci USA. 2004; 101:7833-8). The plantsare analyzed for their overall size, time to flowering, yield, proteincontent of shoot and/or grain. The parameters checked are the overallsize of the mature plant, its wet and dry weight, the weight of theseeds yielded, the average seed size and the number of seeds producedper plant. Other parameters that may be tested are: the chlorophyllcontent of leaves (as nitrogen plant status and the degree of leafverdure is highly correlated), amino acid and the total protein contentof the seeds or other plant parts such as leaves or shoots, oil content,etc. Similarly, instead of providing nitrogen at limiting amounts,phosphate or potassium can be added at increasing concentrations. Again,the same parameters measured are the same as listed above. In this way,nitrogen use efficiency (NUE), phosphate use efficiency (PUE) andpotassium use efficiency (KUE) are assessed, checking the ability of thetransgenic plants to thrive under nutrient restraining conditions.

Nitrogen use efficiency—To analyze whether the transgenic plants (e.g.,Arabidopsis plants) are more responsive to nitrogen, plant are grown in0.75-3 mM (nitrogen deficient conditions) or 6-10 mM (optimal nitrogenconcentration). Plants are allowed to grow for additional 25 days oruntil seed production. The plants are then analyzed for their overallsize, time to flowering, yield, protein content of shoot and/orgrain/seed production. The parameters checked can be the overall size ofthe plant, wet and dry weight, the weight of the seeds yielded, theaverage seed size and the number of seeds produced per plant. Otherparameters that may be tested are: the chlorophyll content of leaves (asnitrogen plant status and the degree of leaf greenness is highlycorrelated), amino acid and the total protein content of the seeds orother plant parts such as leaves or shoots and oil content. Transformedplants not exhibiting substantial physiological and/or morphologicaleffects, or exhibiting higher measured parameters levels than wild-typeplants, are identified as nitrogen use efficient plants.

Nitrogen Use efficiency assay using plantlets—The assay is doneaccording to Yanagisawa-S. et al. with minor modifications (“Metabolicengineering with Dof1 transcription factor in plants: Improved nitrogenassimilation and growth under low-nitrogen conditions” Proc. Natl. Acad.Sci. USA 101, 7833-7838). Briefly, transgenic plants which are grown for7-10 days in 0.5×MS [Murashige-Skoog] supplemented with a selectionagent are transferred to two nitrogen-limiting conditions: MS media inwhich the combined nitrogen concentration (NH₄NO₃ and KNO₃) was 0.75 mM(nitrogen deficient conditions) or 6-15 mM (optimal nitrogenconcentration). Plants are allowed to grow for additional 30-40 days andthen photographed, individually removed from the Agar (the shoot withoutthe roots) and immediately weighed (fresh weight) for later statisticalanalysis. Constructs for which only T1 seeds are available are sown onselective media and at least 20 seedlings (each one representing anindependent transformation event) are carefully transferred to thenitrogen-limiting media. For constructs for which T2 seeds areavailable, different transformation events are analyzed. Usually, 20randomly selected plants from each event are transferred to thenitrogen-limiting media allowed to grow for 3-4 additional weeks andindividually weighed at the end of that period. Transgenic plants arecompared to control plants grown in parallel under the same conditions.Mock-transgenic plants expressing the uidA reporter gene (GUS) under thesame promoter or transgenic plants carrying the same promoter butlacking a reporter gene are used as control.

Nitrogen determination—The procedure for N (nitrogen) concentrationdetermination in the structural parts of the plants involves thepotassium persulfate digestion method to convert organic N to NO₃ ⁻(Purcell and King 1996 Argon. J. 88:111-113, the modified Cd⁻ mediatedreduction of NO₃ ⁻ to NO₂ ⁻ (Vodovotz 1996 Biotechniques 20:390-394) andthe measurement of nitrite by the Griess assay (Vodovotz 1996, supra).The absorbance values are measured at 550 nm against a standard curve ofNaNO₂. The procedure is described in details in Samonte et al. 2006Agron. J. 98:168-176.

Germination tests—Germination tests compare the percentage of seeds fromtransgenic plants that could complete the germination process to thepercentage of seeds from control plants that are treated in the samemanner Normal conditions are considered for example, incubations at 22°C. under 22-hour light 2-hour dark daily cycles. Evaluation ofgermination and seedling vigor is conducted between 4 and 14 days afterplanting. The basal media is 50% MS medium (Murashige and Skoog, 1962Plant Physiology 15, 473-497).

Germination is checked also at unfavorable conditions such as cold(incubating at temperatures lower than 10° C. instead of 22° C.) orusing seed inhibition solutions that contain high concentrations of anosmolyte such as sorbitol (at concentrations of 50 mM, 100 mM, 200 mM,300 mM, 500 mM, and up to 1000 mM) or applying increasing concentrationsof salt (of 50 mM, 100 mM, 200 mM, 300 mM, 500 mM NaCl).

The effect of the transgene on plant's vigor, growth rate, biomass,yield and/or oil content can be determined using known methods.

Plant vigor—The plant vigor can be calculated by the increase in growthparameters such as leaf area, fiber length, rosette diameter, plantfresh weight and the like per time.

Growth rate—The growth rate can be measured using digital analysis ofgrowing plants. For example, images of plants growing in greenhouse onplot basis can be captured every 3 days and the rosette area can becalculated by digital analysis. Rosette area growth is calculated usingthe difference of rosette area between days of sampling divided by thedifference in days between samples.

It should be noted that an increase in rosette parameters such asrosette area, rosette diameter and/or rosette growth rate in a plantmodel such as Arabidopsis predicts an increase in canopy coverage and/orplot coverage in a target plant such as Brassica sp., soy, corn, wheat,Barley, oat, cotton, rice, tomato, sugar beet, and vegetables such aslettuce.

Evaluation of growth rate can be done by measuring plant biomassproduced, rosette area, leaf size or root length per time (can bemeasured in cm² per day of leaf area).

Relative growth area can be calculated using Formula II.

Formula II

Relative growth rate area=Regression coefficient of area along timecourse

Thus, the relative growth area rate is in units of area units (e.g.,mm²/day or cm²/day) and the relative length growth rate is in units oflength units (e.g., cm/day or mm/day).

For example, RGR can be determined for plant height (Formula III), SPAD(Formula IV), Number of tillers (Formula V), root length (Formula VI),vegetative growth (Formula VII), leaf number (Formula VIII), rosettearea (Formula IX), rosette diameter (Formula X), plot coverage (FormulaXI), leaf blade area (Formula XII), and leaf area (Formula XIII).

Formula III: Relative growth rate of Plant height=Regression coefficientof Plant height along time course (measured in cm/day).

Formula IV: Relative growth rate of SPAD=Regression coefficient of SPADmeasurements along time course.

Formula V: Relative growth rate of Number of tillers=Regressioncoefficient of Number of tillers along time course (measured in units of“number of tillers/day”).

Formula VI: Relative growth rate of root length=Regression coefficientof root length along time course (measured in cm per day).

Vegetative growth rate analysis—was calculated according to Formula VIIbelow.

Formula VII: Relative growth rate of vegetative growth=Regressioncoefficient of vegetative dry weight along time course (measured ingrams per day).

Formula VIII: Relative growth rate of leaf number=Regression coefficientof leaf number along time course (measured in number per day).

Formula IX: Relative growth rate of rosette area=Regression coefficientof rosette area along time course (measured in cm² per day).

Formula X: Relative growth rate of rosette diameter=Regressioncoefficient of rosette diameter along time course (measured in cm perday).

Formula XI: Relative growth rate of plot coverage=Regression coefficientof plot (measured in cm² per day).

Formula XII: Relative growth rate of leaf blade area=Regressioncoefficient of leaf area along time course (measured in cm² per day).

Formula XIII: Relative growth rate of leaf area=Regression coefficientof leaf area along time course (measured in cm² per day).

Formula XIV: 1000 Seed Weight=number of seed in sample/sampleweight×1000.

The Harvest Index can be calculated using Formulas XV, XVI, XVII, XVIIIand LXV below.

Formula XV: Harvest Index (seed)=Average seed yield per plant/Averagedry weight.

Formula XVI: Harvest Index (Sorghum)=Average grain dry weight perHead/(Average vegetative dry weight per Head+Average Head dry weight).

Formula XVII: Harvest Index (Maize)=Average grain weight perplant/(Average vegetative dry weight per plant plus Average grain weightper plant).

Harvest Index (for barley)—The harvest index is calculated using FormulaXVIII.

Formula XVIII: Harvest Index (for barley and wheat)=Average spike dryweight per plant/(Average vegetative dry weight per plant+Average spikedry weight per plant).

Following is a non-limited list of additional parameters which can bedetected in order to show the effect of the transgene on the desiredplant's traits:

Formula XIX: Grain circularity=4×3.14 (grain area/perimeter²)

Formula XX: Internode volume=3.14×(d/2)²×1

Formula XXI: Total dry matter (kg)=Normalized head weight perplant+vegetative dry weight.

Formula XXII: Root/Shoot Ratio=total weight of the root at harvest/totalweight of the vegetative portion above ground at harvest. (=RBiH/BiH)

Formula XXIII: Ratio of the number of pods per node on main stem at podset=Total number of pods on main stem/Total number of nodes on mainstem.

Formula XXIV: Ratio of total number of seeds in main stem to number ofseeds on lateral branches=Total number of seeds on main stem at podset/Total number of seeds on lateral branches at pod set.

Formula XXV: Petiole Relative Area=(Petiole area)/Rosette area (measuredin %). Formula XXVI: % reproductive tiller percentage=Number ofReproductive tillers/number of tillers)×100.

Formula XXVII: Spikes Index=Average Spikes weight per plant/(Averagevegetative dry weight per plant plus Average Spikes weight per plant).

Formula XXVIII:

Relative growth rate of root coverage=Regression coefficient of rootcoverage along time course.

Formula XXIX:

Seed Oil yield=Seed yield per plant (gr.)*Oil % in seed.

Formula XXX: shoot/root Ratio=total weight of the vegetative portionabove ground at harvest/total weight of the root at harvest.

Formula XXXI: Spikelets Index=Average Spikelets weight perplant/(Average vegetative dry weight per plant plus Average Spikeletsweight per plant).

Formula XXXII: % Canopy coverage=(1−(PAR_DOWN/PAR_UP))×100 measuredusing AccuPAR Ceptometer Model LP-80.

Formula XXXIII: leaf mass fraction=Leaf area/shoot FW.

Formula XXXIV: Relative growth rate based on dry weight=Regressioncoefficient of dry weight along time course.

Formula XXXV: Dry matter partitioning (ratio)—At the end of the growingperiod 6 plants heads as well as the rest of the plot heads werecollected, threshed and grains were weighted to obtain grains yield perplot. Dry matter partitioning was calculated by dividing grains yieldper plot to vegetative dry weight per plot.

Formula XXXVI: 1000 grain weight filling rate (gr/day)—The rate of grainfilling was calculated by dividing 1000 grain weight by grain fillduration.

Formula XXXVH: Specific leaf area (cm²/gr)—Leaves were scanned to obtainleaf area per plant, and then were dried in an oven to obtain the leavesdry weight. Specific leaf area was calculated by dividing the leaf areaby leaf dry weight.

Formula XXXVIII: Vegetative dry weight per plant at flowering/wateruntil flowering (gr/lit)—Calculated by dividing vegetative dry weight(excluding roots and reproductive organs) per plant at flowering by thewater used for irrigation up to flowering

Formula XXXIX: Yield filling rate (gr/day)—The rate of grain filling wascalculated by dividing grains Yield by grain fill duration.

Formula XXXX: Yield per dunam/water until tan (kg/lit)—Calculated bydividing Grains yield per dunam by water used for irrigation until tan.

Formula XXXXI: Yield per plant/water until tan (gr/lit)—Calculated bydividing Grains yield per plant by water used for irrigation until tan

Formula XXXXII: Yield per dunam/water until maturity (gr/lit)—Calculatedby dividing grains yield per dunam by the water used for irrigation upto maturity. “Lit”=Liter.

Formula XXXXIII: Vegetative dry weight per plant/water until maturity(gr/lit): Calculated by dividing vegetative dry weight per plant(excluding roots and reproductive organs) at harvest by the water usedfor irrigation up to maturity.

Formula XXXXIV: Total dry matter per plant/water until maturity(gr/lit): Calculated by dividing total dry matter at harvest (vegetativeand reproductive, excluding roots) per plant by the water used forirrigation up to maturity.

Formula XXXXV: Total dry matter per plant/water until flowering(gr/lit): Calculated by dividing total dry matter at flowering(vegetative and reproductive, excluding roots) per plant by the waterused for irrigation up to flowering.

Formula XXXXVI: Heads index (ratio): Average heads weight/(Averagevegetative dry weight per plant plus Average heads weight per plant).

Formula XXXXVH: Yield/SPAD (kg/SPAD units)—Calculated by dividing grainsyield by average SPAD measurements per plot.

Formula XXXXVIII: Stem water content (percentage)—stems were collectedand fresh weight (FW) was weighted. Then the stems were oven dry and dryweight (DW) was recorded. Stems dry weight was divided by stems freshweight, subtracted from 1 and multiplied by 100.

Formula XXXXIX: Leaf water content (percentage)—Leaves were collectedand fresh weight (FW) was weighted. Then the leaves were oven dry anddry weight (DW) was recorded. Leaves dry weight was divided by leavesfresh weight, subtracted from 1 and multiplied by 100.

Formula L: stem volume (cm̂3)—The average stem volume was calculated bymultiplying the average stem length by (3.14*((mean lower and upper stemwidth)/2)̂2).

Formula LI: NUE—is the ratio between total grain yield per totalnitrogen (applied+content) in soil.

Formula LII: NUpE—Is the ratio between total plant N content per total N(applied+content) in soil.

Formula LIII: Total NUtE—Is the ratio between total dry matter per Ncontent of total dry matter.

Formula LIV: Stem density—is the ratio between internode dry weight andinternode volume.

Formula LV: Grain NUtE—Is the ratio between grain yield per N content oftotal dry matter

Formula LVI: N harvest index (Ratio)—Is the ratio between nitrogencontent in grain per plant and the nitrogen of whole plant at harvest.

Formula LVH: Biomass production efficiency—is the ratio between plantbiomass and total shoot N.

Formula LVIII: Harvest index (plot) (ratio)—Average seed yield perplot/Average dry weight per plot.

Formula LIX: Relative growth rate of petiole relative area—Regressioncoefficient of petiole relative area along time course (measured in cm²per day).

Formula LX: Yield per spike filling rate (gr/day)—spike filling rate wascalculated by dividing grains yield per spike to grain fill duration.

Formula LXI: Yield per micro plots filling rate (gr/day)—micro plotsfilling rate was calculated by dividing grains yield per micro plots tograin fill duration.

Formula LXII: Grains yield per hectare [ton/ha]—all spikes per plot wereharvested threshed and grains were weighted after sun dry. The resultingvalue was divided by the number of square meters and multiplied by10,000 (10,000 square meters=1 hectare).

Formula LXIII: Total dry matter (for Maize)=Normalized ear weight perplant+vegetative dry weight.

$\begin{matrix}{{{Agronomical}\mspace{14mu} N\; U\; E} = \frac{\begin{matrix}{{{Yield}\mspace{14mu} {per}\mspace{14mu} {plant}\mspace{14mu} ( {{Kg}.} )^{X\mspace{11mu} {Nitrogen}\mspace{11mu} {Fertilization}}} -} \\{{Yield}\mspace{14mu} {per}\mspace{14mu} {plant}\mspace{14mu} ( {{Kg}.} )^{0\% \mspace{11mu} {Nitrogen}\mspace{11mu} {Fertilization}}}\end{matrix}}{{Fertilizer}^{X}}} & {{Formula}\mspace{14mu} {LXIV}}\end{matrix}$

Formula LXV: Harvest Index (brachypodium)=Average grain weight/averagedry (vegetative+spikelet) weight per plant.

Formula LXVI: Harvest Index for Sorghum* (* when the plants were notdried)=FW (fresh weight) Heads/(FW Heads+FW Plants)

Grain protein concentration—Grain protein content (g grain protein m⁻²)is estimated as the product of the mass of grain N (g grain N m⁻²)multiplied by the N/protein conversion ratio of k-5.13 (Mosse 1990,supra). The grain protein concentration is estimated as the ratio ofgrain protein content per unit mass of the grain (g grain protein kg⁻¹grain).

Fiber length—Fiber length can be measured using fibrograph. Thefibrograph system was used to compute length in terms of “Upper HalfMean” length. The upper half mean (UHM) is the average length of longerhalf of the fiber distribution. The fibrograph measures length in spanlengths at a given percentage point (cottoninc (dot)com/ClassificationofCotton/?Pg=4#Length).

According to some embodiments of the invention, increased yield of cornmay be manifested as one or more of the following: increase in thenumber of plants per growing area, increase in the number of ears perplant, increase in the number of rows per ear, number of kernels per earrow, kernel weight, thousand kernel weight (1000-weight), earlength/diameter, increase oil content per kernel and increase starchcontent per kernel.

As mentioned, the increase of plant yield can be determined by variousparameters. For example, increased yield of rice may be manifested by anincrease in one or more of the following: number of plants per growingarea, number of panicles per plant, number of spikelets per panicle,number of flowers per panicle, increase in the seed filling rate,increase in thousand kernel weight (1000-weight), increase oil contentper seed, increase starch content per seed, among others. An increase inyield may also result in modified architecture, or may occur because ofmodified architecture.

Similarly, increased yield of soybean may be manifested by an increasein one or more of the following: number of plants per growing area,number of pods per plant, number of seeds per pod, increase in the seedfilling rate, increase in thousand seed weight (1000-weight), reduce podshattering, increase oil content per seed, increase protein content perseed, among others. An increase in yield may also result in modifiedarchitecture, or may occur because of modified architecture.

Increased yield of canola may be manifested by an increase in one ormore of the following: number of plants per growing area, number of podsper plant, number of seeds per pod, increase in the seed filling rate,increase in thousand seed weight (1000-weight), reduce pod shattering,increase oil content per seed, among others. An increase in yield mayalso result in modified architecture, or may occur because of modifiedarchitecture.

Increased yield of cotton may be manifested by an increase in one ormore of the following: number of plants per growing area, number ofbolls per plant, number of seeds per boll, increase in the seed fillingrate, increase in thousand seed weight (1000-weight), increase oilcontent per seed, improve fiber length, fiber strength, among others. Anincrease in yield may also result in modified architecture, or may occurbecause of modified architecture.

Oil content—The oil content of a plant can be determined by extractionof the oil from the seed or the vegetative portion of the plant.Briefly, lipids (oil) can be removed from the plant (e.g., seed) bygrinding the plant tissue in the presence of specific solvents (e.g.,hexane or petroleum ether) and extracting the oil in a continuousextractor. Indirect oil content analysis can be carried out usingvarious known methods such as Nuclear Magnetic Resonance (NMR)Spectroscopy, which measures the resonance energy absorbed by hydrogenatoms in the liquid state of the sample [See for example, Conway T F.and Earle F R., 1963, Journal of the American Oil Chemists' Society;Springer Berlin/Heidelberg, ISSN: 0003-021X (Print) 1558-9331 (Online)];the Near Infrared (NI) Spectroscopy, which utilizes the absorption ofnear infrared energy (1100-2500 nm) by the sample; and a methoddescribed in WO/2001/023884, which is based on extracting oil a solvent,evaporating the solvent in a gas stream which forms oil particles, anddirecting a light into the gas stream and oil particles which forms adetectable reflected light.

Thus, the present invention is of high agricultural value for promotingthe yield of commercially desired crops (e.g., biomass of vegetativeorgan such as poplar wood, or reproductive organ such as number of seedsor seed biomass).

Any of the transgenic plants described hereinabove or parts thereof maybe processed to produce a feed, meal, protein or oil preparation, suchas for ruminant animals.

The transgenic plants described hereinabove, which exhibit an increasedoil content can be used to produce plant oil (by extracting the oil fromthe plant).

The plant oil (including the seed oil and/or the vegetative portion oil)produced according to the method of the invention may be combined with avariety of other ingredients. The specific ingredients included in aproduct are determined according to the intended use. Exemplary productsinclude animal feed, raw material for chemical modification,biodegradable plastic, blended food product, edible oil, biofuel,cooking oil, lubricant, biodiesel, snack food, cosmetics, andfermentation process raw material.

Exemplary products to be incorporated to the plant oil include animalfeeds, human food products such as extruded snack foods, breads, as afood binding agent, aquaculture feeds, fermentable mixtures, foodsupplements, sport drinks, nutritional food bars, multi-vitaminsupplements, diet drinks, and cereal foods.

According to some embodiments of the invention, the oil comprises a seedoil.

According to some embodiments of the invention, the oil comprises avegetative portion oil (oil of the vegetative portion of the plant).

According to some embodiments of the invention, the plant cell forms apart of a plant.

According to another embodiment of the present invention, there isprovided a food or feed comprising the plants or a portion thereof ofthe present invention.

As used herein the term “about” refers to ±10%.

The terms “comprises”, “comprising”, “includes”, “including”, “having”and their conjugates mean “including but not limited to”.

The term “consisting of” means “including and limited to”.

The term “consisting essentially of” means that the composition, methodor structure may include additional ingredients, steps and/or parts, butonly if the additional ingredients, steps and/or parts do not materiallyalter the basic and novel characteristics of the claimed composition,method or structure.

As used herein, the singular form “a”, “an” and “the” include pluralreferences unless the context clearly dictates otherwise. For example,the term “a compound” or “at least one compound” may include a pluralityof compounds, including mixtures thereof.

Throughout this application, various embodiments of this invention maybe presented in a range format. It should be understood that thedescription in range format is merely for convenience and brevity andshould not be construed as an inflexible limitation on the scope of theinvention. Accordingly, the description of a range should be consideredto have specifically disclosed all the possible subranges as well asindividual numerical values within that range. For example, descriptionof a range such as from 1 to 6 should be considered to have specificallydisclosed subranges such as from 1 to 3, from 1 to 4, from 1 to 5, from2 to 4, from 2 to 6, from 3 to 6 etc., as well as individual numberswithin that range, for example, 1, 2, 3, 4, 5, and 6. This appliesregardless of the breadth of the range.

Whenever a numerical range is indicated herein, it is meant to includeany cited numeral (fractional or integral) within the indicated range.The phrases “ranging/ranges between” a first indicate number and asecond indicate number and “ranging/ranges from” a first indicate number“to” a second indicate number are used herein interchangeably and aremeant to include the first and second indicated numbers and all thefractional and integral numerals therebetween.

As used herein the term “method” refers to manners, means, techniquesand procedures for accomplishing a given task including, but not limitedto, those manners, means, techniques and procedures either known to, orreadily developed from known manners, means, techniques and proceduresby practitioners of the chemical, pharmacological, biological,biochemical and medical arts.

When reference is made to particular sequence listings, such referenceis to be understood to also encompass sequences that substantiallycorrespond to its complementary sequence as including minor sequencevariations, resulting from, e.g., sequencing errors, cloning errors, orother alterations resulting in base substitution, base deletion or baseaddition, provided that the frequency of such variations is less than 1in 50 nucleotides, alternatively, less than 1 in 100 nucleotides,alternatively, less than 1 in 200 nucleotides, alternatively, less than1 in 500 nucleotides, alternatively, less than 1 in 1000 nucleotides,alternatively, less than 1 in 5,000 nucleotides, alternatively, lessthan 1 in 10,000 nucleotides.

It is appreciated that certain features of the invention, which are, forclarity, described in the context of separate embodiments, may also beprovided in combination in a single embodiment. Conversely, variousfeatures of the invention, which are, for brevity, described in thecontext of a single embodiment, may also be provided separately or inany suitable subcombination or as suitable in any other describedembodiment of the invention. Certain features described in the contextof various embodiments are not to be considered essential features ofthose embodiments, unless the embodiment is inoperative without thoseelements.

Various embodiments and aspects of the present invention as delineatedhereinabove and as claimed in the claims section below find experimentalsupport in the following examples.

EXAMPLES

Reference is now made to the following examples, which together with theabove descriptions illustrate some embodiments of the invention in a nonlimiting fashion.

Generally, the nomenclature used herein and the laboratory proceduresutilized in the present invention include molecular, biochemical,microbiological and recombinant DNA techniques. Such techniques arethoroughly explained in the literature. See, for example, “MolecularCloning: A laboratory Manual” Sambrook et al., (1989); “CurrentProtocols in Molecular Biology” Volumes I-III Ausubel, R. M., ed.(1994); Ausubel et al., “Current Protocols in Molecular Biology”, JohnWiley and Sons, Baltimore, Md. (1989); Perbal, “A Practical Guide toMolecular Cloning”, John Wiley & Sons, New York (1988); Watson et al.,“Recombinant DNA”, Scientific American Books, New York; Birren et al.(eds) “Genome Analysis: A Laboratory Manual Series”, Vols. 1-4, ColdSpring Harbor Laboratory Press, New York (1998); methodologies as setforth in U.S. Pat. Nos. 4,666,828; 4,683,202; 4,801,531; 5,192,659 and5,272,057; “Cell Biology: A Laboratory Handbook”, Volumes I-III Cellis,J. E., ed. (1994); “Current Protocols in Immunology” Volumes I-IIIColigan J. E., ed. (1994); Stites et al. (eds), “Basic and ClinicalImmunology” (8th Edition), Appleton & Lange, Norwalk, Conn. (1994);Mishell and Shiigi (eds), “Selected Methods in Cellular Immunology”, W.H. Freeman and Co., New York (1980); available immunoassays areextensively described in the patent and scientific literature, see, forexample, U.S. Pat. Nos. 3,791,932; 3,839,153; 3,850,752; 3,850,578;3,853,987; 3,867,517; 3,879,262; 3,901,654; 3,935,074; 3,984,533;3,996,345; 4,034,074; 4,098,876; 4,879,219; 5,011,771 and 5,281,521;“Oligonucleotide Synthesis” Gait, M. J., ed. (1984); “Nucleic AcidHybridization” Hames, B. D., and Higgins S. J., eds. (1985);“Transcription and Translation” Hames, B. D., and Higgins S. J., Eds.(1984); “Animal Cell Culture” Freshney, R. I., ed. (1986); “ImmobilizedCells and Enzymes” IRL Press, (1986); “A Practical Guide to MolecularCloning” Perbal, B., (1984) and “Methods in Enzymology” Vol. 1-317,Academic Press; “PCR Protocols: A Guide To Methods And Applications”,Academic Press, San Diego, Calif. (1990); Marshak et al., “Strategiesfor Protein Purification and Characterization—A Laboratory CourseManual” CSHL Press (1996); all of which are incorporated by reference asif fully set forth herein. Other general references are providedthroughout this document. The procedures therein are believed to be wellknown in the art and are provided for the convenience of the reader. Allthe information contained therein is incorporated herein by reference.

General Experimental and Bioinformatics Methods

RNA extraction—Tissues growing at various growth conditions (asdescribed below) were sampled and RNA was extracted using TRIzol Reagentfrom Invitrogen [invitrogen (dot) com/content (dot)cfm?pageid=469].Approximately 30-50 mg of tissue was taken from samples. The weighedtissues were ground using pestle and mortar in liquid nitrogen andresuspended in 500 μl of TRIzol Reagent. To the homogenized lysate, 100μl of chloroform was added followed by precipitation using isopropanoland two washes with 75% ethanol. The RNA was eluted in 30 μl ofRNase-free water. RNA samples were cleaned up using Qiagen's RNeasyminikit clean-up protocol as per the manufacturer's protocol (QIAGENInc, CA USA). For convenience, each micro-array expression informationtissue type has received an expression Set ID.

Correlation analysis—was performed for selected genes according to someembodiments of the invention, in which the characterized parameters(measured parameters according to the correlation IDs) were used as “Xaxis” for correlation with the tissue transcriptome, which was used asthe “Y axis”. For each gene and measured parameter a correlationcoefficient “R” was calculated (using Pearson correlation) along with ap-value for the significance of the correlation. When the correlationcoefficient (R) between the levels of a gene's expression in a certaintissue and a phenotypic performance across ecotypes/variety/hybrid ishigh in absolute value (between 0.5-1), there is an association betweenthe gene (specifically the expression level of this gene) and thephenotypic characteristic (e g, improved yield, growth rate, nitrogenuse efficiency, abiotic stress tolerance and the like).

Example 1 Identifying Genes which Improve Yield and AgronomicalImportant Traits in Plants

The present inventors have identified polynucleotides which expressionthereof in plants can increase yield, fiber yield, fiber quality, growthrate, vigor, biomass, growth rate, oil content, abiotic stress tolerance(ABST), fertilizer use efficiency (FUE) such as nitrogen use efficiency(NUE), and water use efficiency (WUE) of a plant, as follows.

All nucleotide sequence datasets used here were originated from publiclyavailable databases or from performing sequencing using the Solexatechnology (e.g. Barley and Sorghum). Sequence data from 100 differentplant species was introduced into a single, comprehensive database.Other information on gene expression, protein annotation, enzymes andpathways were also incorporated.

Major databases used include:

Genomes

Arabidopsis genome [TAIR genome version 6 (arabidopsis (dot) org/)];

Rice genome [IRGSP build 4.0 (rgp (dot) dna (dot) affrc (dot) go (dot)jp/IRGSP/)];

Poplar [Populus trichocarpa release 1.1 from JGI (assembly release v1.0)(genome (dot) jgi-psf (dot) org/)];

Brachypodium [JGI 4× assembly, brachpodium (dot) org)];

Soybean [DOE-JGI SCP, version GlymaO (phytozome (dot) net/)];

Grape [French-Italian Public Consortium for Grapevine GenomeCharacterization grapevine genome (genoscope (dot) cns (dot) fr/)];

Castobean [TIGR/J Craig Venter Institute 4× assembly [msc (dot) jcvi(dot) org/r communis];

Sorghum [DOE-JGI SCP, version Sbi1 [phytozome (dot) net/)];

Partially assembled genome of Maize [maizesequence (dot) org/];

Expressed EST and mRNA sequences were extracted from the followingdatabases:

GenBank ncbi (dot) nlm (dot) nih (dot) gov/dbEST;

RefSeq (ncbi (dot) nlm (dot) nih (dot) gov/RefSeq/);

TAIR (arabidopsis (dot) org/);

Protein and Pathway Databases

Uniprot [uniprot (dot) org/];

AraCyc [arabidopsis (dot) org/biocyc/index (dot) jsp];

ENZYME [expasy (dot) org/enzyme/];

Microarray Datasets were Downloaded from:

GEO (ncbi.nlm.nih gov/geo/);

TAIR (arabidopsis.org/);

Proprietary microarray data (WO2008/122980);

QTL and SNPs Information

Gramene [gramene (dot) org/qtl/];

Panzea [panzea (dot) org/index (dot) html];

Database Assembly—was performed to build a wide, rich, reliableannotated and easy to analyze database comprised of publicly availablegenomic mRNA, ESTs DNA sequences, data from various crops as well asgene expression, protein annotation and pathway data QTLs, and otherrelevant information.

Database assembly is comprised of a toolbox of gene refining,structuring, annotation and analysis tools enabling to construct atailored database for each gene discovery project. Gene refining andstructuring tools enable to reliably detect splice variants andantisense transcripts, generating understanding of various potentialphenotypic outcomes of a single gene. The capabilities of the “LEADS”platform of Compugen LTD for analyzing human genome have been confirmedand accepted by the scientific community [see e.g., “WidespreadAntisense Transcription”, Yelin, et al. (2003) Nature Biotechnology 21,379-85; “Splicing of Alu Sequences”, Lev-Maor, et al. (2003) Science 300(5623), 1288-91; “Computational analysis of alternative splicing usingEST tissue information”, Xie H et al. Genomics 2002], and have beenproven most efficient in plant genomics as well.

EST clustering and gene assembly—For gene clustering and assembly oforganisms with available genome sequence data (arabidopsis, rice,castorbean, grape, brachypodium, poplar, soybean, sorghum) the genomicLEADS version (GANG) was employed. This tool allows most accurateclustering of ESTs and mRNA sequences on genome, and predicts genestructure as well as alternative splicing events and anti-sensetranscription.

For organisms with no available full genome sequence data, “expressedLEADS” clustering software was applied.

Gene annotation—Predicted genes and proteins were annotated as follows:

Blast search [blast (dot) ncbi (dot) nlm (dot) nih (dot) gov/Blast (dot)cgi] against all plant UniProt [uniprot (dot) org/] sequences wasperformed. Open reading frames of each putative transcript were analyzedand longest ORF with higher number of homologues was selected aspredicted protein of the transcript. The predicted proteins wereanalyzed by InterPro [ebi (dot) ac (dot) uk/interpro/].

Blast against proteins from AraCyc and ENZYME databases was used to mapthe predicted transcripts to AraCyc pathways.

Predicted proteins from different species were compared using blastalgorithm [ncbi (dot) nlm (dot) nih (dot) gov/Blast (dot) cgi] tovalidate the accuracy of the predicted protein sequence, and forefficient detection of orthologs.

Gene expression profiling—Several data sources were exploited for geneexpression profiling, namely microarray data and digital expressionprofile (see below). According to gene expression profile, a correlationanalysis was performed to identify genes which are co-regulated underdifferent development stages and environmental conditions and associatedwith different phenotypes.

Publicly available microarray datasets were downloaded from TAIR andNCBI GEO sites, renormalized, and integrated into the database.Expression profiling is one of the most important resource data foridentifying genes important for yield.

A digital expression profile summary was compiled for each clusteraccording to all keywords included in the sequence records comprisingthe cluster. Digital expression, also known as electronic Northern Blot,is a tool that displays virtual expression profile based on the ESTsequences forming the gene cluster. The tool provides the expressionprofile of a cluster in terms of plant anatomy (e.g., the tissue/organin which the gene is expressed), developmental stage (the developmentalstages at which a gene can be found) and profile of treatment (providesthe physiological conditions under which a gene is expressed such asdrought, cold, pathogen infection, etc). Given a random distribution ofESTs in the different clusters, the digital expression provides aprobability value that describes the probability of a cluster having atotal of N ESTs to contain X ESTs from a certain collection oflibraries. For the probability calculations, the following is taken intoconsideration: a) the number of ESTs in the cluster, b) the number ofESTs of the implicated and related libraries, c) the overall number ofESTs available representing the species. Thereby clusters with lowprobability values are highly enriched with ESTs from the group oflibraries of interest indicating a specialized expression.

Recently, the accuracy of this system was demonstrated by Portnoy etal., 2009 (Analysis Of The Melon Fruit Transcriptome Based On 454Pyrosequencing) in: Plant & Animal Genomes XVII Conference, San Diego,Calif. Transcriptomeic analysis, based on relative EST abundance in datawas performed by 454 pyrosequencing of cDNA representing mRNA of themelon fruit. Fourteen double strand cDNA samples obtained from twogenotypes, two fruit tissues (flesh and rind) and four developmentalstages were sequenced. GS FLX pyrosequencing (Roche/454 Life Sciences)of non-normalized and purified cDNA samples yielded 1,150,657 expressedsequence tags, that assembled into 67,477 unigenes (32,357 singletonsand 35,120 contigs). Analysis of the data obtained against the CucurbitGenomics Database [icugi (dot) org/] confirmed the accuracy of thesequencing and assembly. Expression patterns of selected genes fittedwell their qRT-PCR data.

The genes listed in Table 1 below were identified to have a major impacton plant yield, fiber yield, fiber quality, growth rate, photosyntheticcapacity, vigor, biomass, growth rate, oil content, abiotic stresstolerance, nitrogen use efficiency, water use efficiency and/orfertilizer use efficiency when expression thereof is increased inplants. The identified genes, their curated polynucleotide andpolypeptide sequences, their updated sequences according to Genbankdatabase and the sequences of the cloned genes and proteins aresummarized in Table 1, hereinbelow.

TABLE 1 Identified genes for increasing yield, growth rate, vigor,biomass, growth rate, oil content, fiber yield, fiber quality,photosynthetic capacity, abiotic stress tolerance, nitrogen useefficiency, water use efficiency and fertilizer use efficiency of aplant Gene Polyn SEQ ID Polyp. SEQ Name Organism and Cluster tag NO: IDNO: LGP1 arabidopsis|10v1|AT1G32060 4 713 LGP3arabidopsis|10v1|AT1G63680 5 714 LGP6 arabidopsis|10v1|AT2G25080 6 715LGP8 arabidopsis|10v1|AT3G13720 7 716 LGP9 arabidopsis|10v1|AT3G17810 8717 LGP10 arabidopsis|10v1|AT3G20330 9 718 LGP12arabidopsis|10v1|AT3G54660 10 719 LGP18 arabidopsis|10v1|AT5G57030 11720 LGP19 b_juncea|10v2|E6ANDIZ01AHMLF 12 721 LGP20 barley|10v2|AV83385713 722 LGP21 barley|10v2|BG367409 14 723 LGP22 barley|10v2|BI960336 15724 LGP24 lettuce|10v1|AF321538 16 725 LGP25 maize|10v1|AI622096 17 726LGP27 maize|10v1|BG360609 18 727 LGP32 tomato|11v1|AF030292 19 728 LGP34tomato|11v1|BG131753 20 729 LGP35 tomato|11v1|R27545 21 730 LGP38arabidopsis|10v1|AT2G15400 22 731 LGP39 arabidopsis|10v1|AT2G15430 23732 LGP41 sunflower|12v1|CD855665 24 733 LGP42 tomato|11v1|BG128831 25734 LGP43 canola|11v1|EG019929 26 735 LGP44 arabidopsis|10v1|AT5G3731027 736 LGP45 b_juncea|10v2|E6ANDIZ01A3IC5 28 737 LGP46arabidopsis|10v1|AT5G58140 29 738 LGP47 cotton|11v1|CO074926XX1 30 739LGP48 canola|11v1|EG020435 31 740 LGP49 canola|11v1|EE457807 32 741LGP52 sorghum|12v1|SB05G024560 33 742 LGP53 arabidopsis|10v1|AT5G4562034 743 LGP54 canola|11v1|AY518886 35 744 LGP58 cotton|11v1|BQ405024 36745 LGP59 arabidopsis|10v1|AT3G06430 37 746 LGP60pigeonpea|11v1|SRR054580X101438 38 747 LGP61 sesame|12v1|SESI12V141279539 748 LGP62 cephalotaxus|11v1|SRR064395X102206 40 749 LGP63rice|11v1|BI305215 41 750 LGP64 flaveria||11v1|SRR149229.109105 42 751LGP65 cotton|11v1|CO084001 43 752 LGP66 physcomitrella||10v1|BJ172182 44753 LGP67 canola|11v1|DW997362 45 754 LGP68 rice|11v1|AB042521 46 755LGP69 canola|11v1|EV020542 47 756 LGP71 bean|12v1|CA896692 48 757 LGP72maize|10v1|AI967029 49 758 LGP73 maize|10v1|AW054577 50 759 LGP74maize|10v1|BM075120 51 760 LGP75 maize|10v1|ZMU12233 52 761 LGP76rice|11v1|AU056832 53 762 LGP77 rice|11v1|BE040832 54 763 LGP78soybean|11v1|GLYMA04G40990 55 764 LGP79 soybean|11v1|GLYMA18G17600 56765 LGP80 maize|10v1|BM500498 57 766 LGP81 soybean|11v1|GLYMA09G02440 58767 LGP82 maize|10v1|AI964481 59 768 LGP83 barley|12v1|BE412944 60 769LGP84 bean|12v2|CA900203 61 770 LGP85 bean|12v2|FE697169 62 771 LGP86maize|10v1|AA979831 63 772 LGP87 maize|10v1|AI461460 64 773 LGP88maize|10v1|AI612489 65 774 LGP89 maize|10v1|AI783343 66 775 LGP90maize|10v1|AI855400 67 776 LGP91 maize|10v1|AI943931 68 777 LGP92maize|10v1|AW018130 69 778 LGP93 maize|10v1|AW400247 70 779 LGP94maize|10v1|BE186218 71 780 LGP95 maize|10v1|BE511836 72 781 LGP96medicago||12v1|AI083076 73 782 LGP97 medicago||12v1|AW687978 74 783LGP98 medicago||12v1|BE249345 75 784 LGP99 rice|11v1|AI978381 76 785LGP100 rice|11v1|AU100980 77 786 LGP101 rice|11v1|BM038323 78 787 LGP102sorghum|12v1|SB01G004630 79 788 LGP103 sorghum|12v1|SB04G021670 80 789LGP104 soybean|11v1|GLYMA05G04590 81 790 LGP105soybean|12v1|GLYMA11G31810 82 791 LGP106 soybean|13v2|BU577083 83 792LGP107 tomato|11v1|AW221249 84 793 LGP108 wheat|12v3|AL826289 85 794LGP109 soybean|13v2|GLYMA16G02770T2 86 795 LYD237arabidopsis|10v1|AT5G42190 88 797 MGP14 arabidopsis|10v1|AT5G42190 88797 LYD694 b_juncea|12v1|E6ANDIZ01A6E3M 100 809 LYD695b_juncea|12v1|E6ANDIZ01A8U9K 101 810 LYD696 b_juncea|12v1|E6ANDIZ01DJK4B102 811 LYD698 b_rapa|11v|CD812301 103 812 LYD699 b_rapa|11v|CD815849104 813 LYD700 b_rapa|11v|CD829408 105 814 LYD701 bean|12v1|CA913107 106815 LYD702 bean|12v2|AB020052 107 816 LYD703 bean|12v2|CA896596 108 817LYD704 bean|12v2|CA896633 109 818 LYD705 bean|12v2|CA896897 110 819LYD706 bean|12v2|CA896947 111 820 LYD707 bean|12v2|CA897026 112 821LYD708 bean|12v2|CA897554 113 822 LYD710 bean|12v2|CA898557 114 823LYD711 bean|12v2|CA898580 115 824 LYD713 bean|12v2|CA898845 116 825LYD714 bean|12v2|CA898855 117 826 LYD715 bean|12v2|CA899048 118 827LYD717 bean|12v2|CA899256 119 828 LYD718 bean|12v2|CA899264 120 829LYD719 bean|12v2|CA899770 121 830 LYD720 bean|12v2|CA899773 122 831LYD721 bean|12v2|CA900278 123 832 LYD722 bean|12v2|CA900376 124 833LYD723 bean|12v2|CA900579 125 834 LYD725 bean|12v2|CA900816 126 835LYD726 bean|12v2|CA901228 127 836 LYD727 bean|12v2|CA902441 128 837LYD729 bean|12v2|CA902538 129 838 LYD730 bean|12v2|CA905289 130 839LYD731 bean|12v2|CA905720 131 840 LYD733 bean|12v2|CA906136 132 841LYD735 bean|12v2|CA906321 133 842 LYD736 bean|12v2|CA906920 134 843LYD737 bean|12v2|CA908547 135 844 LYD738 bean|12v2|CA909218 136 845LYD739 bean|12v2|CA909651 137 846 LYD740 bean|12v2|CA910570 138 847LYD741 bean|12v2|CA910581 139 848 LYD742 bean|12v2|CA910778 140 849LYD744 bean|12v2|CA911083 141 850 LYD745 bean|12v2|CA911177 142 851LYD746 bean|12v2|CA911180 143 852 LYD747 bean|12v2|CA911414 144 853LYD748 bean|12v2|CA911651 145 854 LYD749 bean|12v2|CA911692 146 855LYD750 bean|12v2|CA911987 147 856 LYD751 bean|12v2|CA911994 148 857LYD752 bean|12v2|CA912567 149 858 LYD753 bean|12v2|CA912688 150 859LYD754 bean|12v2|CA912714 151 860 LYD755 bean|12v2|CA913041 152 861LYD756 bean|12v2|CA913114 153 862 LYD757 bean|12v2|CA913188 154 863LYD758 bean|12v2|CA913400 155 864 LYD760 bean|12v2|CA913671 156 865LYD761 bean|12v2|CA913893 157 866 LYD762 bean|12v2|CA915895 158 867LYD763 bean|12v2|CA915968 159 868 LYD764 bean|12v2|CA916036 160 869LYD765 bean|12v2|CA916308 161 870 LYD767 bean|12v2|CA916492 162 871LYD768 bean|12v2|CA916620 163 872 LYD769 bean|12v2|CB280523 164 873LYD771 bean|12v2|CB539357 165 874 LYD772 bean|12v2|CB539439 166 875LYD773 bean|12v2|CB539539 167 876 LYD774 bean|12v2|CB539605 168 877LYD776 bean|12v2|CB540092 169 878 LYD777 bean|12v2|CB540540 170 879LYD778 bean|12v2|CB540751 171 880 LYD779 bean|12v2|CB540835 172 881LYD780 bean|12v2|CB540856 173 882 LYD781 bean|12v2|CB541126 174 883LYD782 bean|12v2|CB541134 175 884 LYD783 bean|12v2|CB541623 176 885LYD784 bean|12v2|CB542381 177 886 LYD785 bean|12v2|CB542514 178 887LYD786 bean|12v2|CB543395 179 888 LYD788 bean|12v2|EG562919 180 889LYD789 bean|12v2|EX303656 181 890 LYD790 bean|12v2|EX304540 182 891LYD791 bean|12v2|EX304854 183 892 LYD792 bean|12v2|EX304918 184 893LYD793 bean|12v2|EX305451 185 894 LYD794 bean|12v2|FE677973 186 895LYD795 bean|12v2|FE683224 187 896 LYD796 bean|12v2|FE684083 188 897LYD797 bean|12v2|FE686354 189 898 LYD798 bean|12v2|FE696773 190 899LYD799 bean|12v2|FE707538 191 900 LYD800 bean|12v2|FE708889 192 901LYD801 bean|12v2|FE897943 193 902 LYD802 bean|12v2|FE898020 194 903LYD803 bean|12v2|FE898128 195 904 LYD804 bean|12v2|FE898192 196 905LYD806 bean|12v2|FE898946 197 906 LYD807 bean|12v2|FE898965 198 907LYD809 bean|12v2|FE899199 199 908 LYD810 bean|12v2|FE899532 200 909LYD811 bean|12v2|FE899588 201 910 LYD812 bean|12v2|FG228526 202 911LYD813 bean|12v2|FG228626 203 912 LYD814 bean|12v2|FG230712 204 913LYD815 bean|12v2|FG231267 205 914 LYD816 bean|12v2|FG231286 206 915LYD817 bean|12v2|HO778627 207 916 LYD818 bean|12v2|HO781301 208 917LYD819 bean|12v2|HO783841 209 918 LYD821 bean|12v2|HO790120 210 919LYD822 bean|12v2|HO792571 211 920 LYD823 bean|12v2|HO793451 212 921LYD824 bean|12v2|HO799789 213 922 LYD825 bean|12v2|HO806735 214 923LYD826 bean|12v2|HO807062 215 924 LYD827bean|12v2|PVJGI_V1_2012PHVUL_011G043200_1_PACID_27151804 216 925 LYD828bean|13v1|CA914375 217 926 LYD829 bean|13v1|CB544235 218 927 LYD830bean|13v1|FE690778 219 928 LYD831 canola|11v1|CN730435 220 929 LYD833canola|11v1|EE424371 221 930 LYD834 canola|11v1|EE482584 222 931 LYD835cotton|11v1|AI055088 223 932 LYD836 cotton|11v1|AI729950 224 933 LYD837cotton|11v1|AY779339XX1 225 934 LYD838 cotton|11v1|BE052016XX1 226 935LYD839 cotton|11v1|BE055237 227 936 LYD840 cotton|11v1|BG444757 228 937LYD841 cotton|11v1|BM359931 229 938 LYD842 cotton|11v1|CB350435XX2 230939 LYD843 cotton|11v1|CD485677 231 940 LYD844 cotton|11v1|CO075283 232941 LYD845 cotton|11v1|CO085527XX2 233 942 LYD846 cotton|11v1|CO089064234 943 LYD847 cotton|11v1|CO112877XX1 235 944 LYD848cotton|11v1|CO121493XX1 236 945 LYD849 cotton|11v1|CO493081 237 946LYD850 cotton|11v1|DW500116 238 947 LYD851 medicago||12v1|AL386155 239948 LYD852 medicago||12v1|AW256362 240 949 LYD853medicago||12v1|AW683324 241 950 LYD854 medicago||12v1|AW696146 242 951LYD855 medicago||12v1|BE316923 243 952 LYD856 medicago||12v1|BF643539244 953 LYD857 medicago||12v1|BF644247 245 954 LYD858 rice|11v1|AA754378246 955 LYD859 rice|13v2|BE228731 247 956 LYD860soybean|11v1|GLYMA13G44040 248 957 LYD861 soybean|11v1|GLYMA15G01270 249958 LYD863 soybean|12v1|GLYMA01G38410 250 959 LYD864soybean|12v1|GLYMA05G25960 251 960 LYD865 soybean|12v1|GLYMA06G46850 252961 LYD866 soybean|12v1|GLYMA08G11220 253 962 LYD867soybean|12v1|GLYMA10G07340 254 963 LYD868 soybean|12v1|GLYMA10G36220 255964 LYD869 soybean|12v1|GLYMA10G36230 256 965 LYD870soybean|12v1|GLYMA11G26980 257 966 LYD871 soybean|12v1|GLYMA11G37390T2258 967 LYD872 soybean|12v1|GLYMA12G36480 259 968 LYD873soybean|12v1|GLYMA14G09990 260 969 LYD874 soybean|12v1|GLYMA14G37920 261970 LYD876 soybean|12v1|GLYMA17G07450 262 971 LYD877soybean|12v1|GLYMA17G12750T4 263 972 LYD878 soybean|12v1|GLYMA17G13780264 973 LYD879 soybean|12v1|GLYMA18G01820 265 974 LYD880soybean|12v1|GLYMA18G01830 266 975 LYD881 soybean|12v1|GLYMA18G48300 267976 LYD882 soybean|12v1|GLYMA18G52810 268 977 LYD883soybean|13v2|GLYMA01G44970 269 978 LYD884 soybean|13v2|GLYMA02G40770 270979 LYD886 soybean|13v2|GLYMA11G20080 271 980 LYD887soybean|13v2|GLYMA12G07990 272 981 LYD888 soybean|13v2|GLYMA13G21490 273982 LYD890 soybean|13v2|GLYMA17G35060 274 983 LYD891soybean|13v2|GLYMA19G40580 275 984 LYD892 tomato|11v1|AF096246 276 985LYD893 tomato|11v1|AI486717 277 986 LYD894 tomato|11v1|AI490031 278 987LYD895 tomato|11v1|AI637290 279 988 LYD896 tomato|11v1|AI771350 280 989LYD897 tomato|11v1|AI773083 281 990 LYD898 tomato|11v1|AI773883 282 991LYD899 tomato|11v1|AI896477 283 992 LYD900 tomato|11v1|AW091881 284 993LYD901 tomato|11v1|AW217431 285 994 LYD902 tomato|11v1|AW399640 286 995LYD903 tomato|11v1|AW624231 287 996 LYD904 tomato|11v1|BG123561 288 997LYD905 tomato|11v1|BG123981 289 998 LYD906 tomato|11v1|BG125291 290 999LYD907 tomato|11v1|BG125405 291 1000 LYD908 tomato|11v1|BG127430 2921001 LYD909 tomato|11v1|BG128668 293 1002 LYD910 tomato|11v1|BG129449294 1003 LYD911 tomato|11v1|BG131325 295 1004 LYD912tomato|11v1|BG132078 296 1005 LYD913 tomato|11v1|BG132886 297 1006LYD914 tomato|11v1|BG628916 298 1007 LYD915 tomato|13v1|AI483969 2991008 LYD917 tomato|13v1|AI774553 300 1009 LYD918 tomato|13v1|AI776834301 1010 LYD919 tomato|13v1|AW160097 302 1011 LYD920tomato|13v1|AW616349 303 1012 LYD921 tomato|13v1|BG128290 304 1013LYD922 tomato|13v1|BG133370 305 1014 LYD923 tomato|13v1|BG627938 3061015 LYD924 tomato|13v1|BG735361 307 1016 LYD925 tomato|13v1|LEACS6 3081017 LYD926 bean|12v2|CA899181 309 1018 LYD929 bean|12v2|CA910968 3101019 LYD930 bean|12v2|CB542591 311 1020 LYD869_H1soybean|13v2|GLYMA20G31360 312 1021 MGP1 cotton|11v1|CO100059XX2 3201029 MGP2 arabidopsis|10v1|AT1G75950 321 1030 MGP4soybean|12v1|GLYMA04G37510 322 1031 MGP5 medicago||12v1|AL374833 3231032 MGP6 brachypodium|12v1|BRADI5G22260 324 1033 MGP7sorghum|12v1|SB03G041200 325 1034 MGP9 switchgrass|12v1|FL691989 3261035 LGP85 bean|12v1|FE697169 327 771 LGP91 maize|10v1|AI943931 328 1036LGP92 maize|10v1|AW018130 329 778 LGP93 maize|10v1|AW400247 330 779LGP104 soybean|11v1|GLYMA05G04590 331 1037 LGP108 wheat|12v3|AL826289332 794 LYD695 b_juncea|12v1|E6ANDIZ01A8U9K 333 1038 LYD696b_juncea|12v1|E6ANDIZ01DJK4B 334 1039 LYD699 b_rapa|11v1|CD815849 3351040 LYD703 bean|12v2|CA896596 336 817 LYD706 bean|12v2|CA896947 337 820LYD707 bean|12v2|CA897026 338 821 LYD715 bean|12v2|CA899048 339 827LYD717 bean|12v2|CA899256 340 828 LYD725 bean|12v2|CA900816 341 1041LYD736 bean|12v2|CA906920 342 1042 LYD737 bean|12v2|CA908547 343 844LYD741 bean|12v2|CA910581 344 1043 LYD751 bean|12v2|CA911994 345 857LYD756 bean|12v2|CA913114 346 862 LYD765 bean|12v2|CA916308 347 870LYD771 bean|12v2|CB539357 348 1044 LYD773 bean|12v2|CB539539 349 1045LYD782 bean|12v2|CB541134 350 884 LYD790 bean|12v2|EX304540 351 891LYD794 bean|12v2|FE677973 352 1046 LYD795 bean|12v2|FE683224 353 896LYD796 bean|12v2|FE684083 354 1047 LYD798 bean|12v2|FE696773 355 899LYD799 bean|12v2|FE707538 356 900 LYD800 bean|12v2|FE708889 357 901LYD801 bean|12v2|FE897943 358 902 LYD803 bean|12v2|FE898128 359 904LYD804 bean|12v2|FE898192 360 905 LYD817 bean|12v2|HO778627 361 916LYD819 bean|12v2|HO783841 362 918 LYD822 bean|12v2|HO792571 363 1048LYD823 bean|12v2|HO793451 364 1049 LYD827bean|12v2|PVJGI_V1_2012PHVUL_011G043200_1_PACID_27151804 365 925 LYD828bean|13v1|CA914375 366 1050 LYD830 bean|13v1|FE690778 367 1051 LYD834canola|11v1|EE482584 368 1052 LYD835 cotton|11v1|AI055088 369 932 LYD841cotton|11v1|BM359931 370 1053 LYD849 cotton|11v1|CO493081 371 946 LYD850cotton|11v1|DW500116 372 947 LYD853 medicago||12v1|AW683324 373 950LYD857 medicago||12v1|BF644247 374 1054 LYD867soybean|12v1|GLYMA10G07340 375 963 LYD868 soybean|12v1|GLYMA10G36220 376964 LYD892 tomato|11v1|AF096246 377 1055 LYD899 tomato|11v1|AI896477 3781056 LYD901 tomato|11v1|AW217431 379 1057 LYD904 tomato|11v1|BG123561380 1058 LYD906 tomato|11v1|BG125291 381 1059 LYD907tomato|11v1|BG125405 382 1060 LYD908 tomato|11v1|BG127430 383 1061LYD910 tomato|11v1|BG129449 384 1062 LYD914 tomato|11v1|BG628916 3851063 LYD915 tomato|11v1|TOBBCSO 386 1008 LYD918 tomato|13v1|AI776834 3871010 LYD921 tomato|13v1|BG128290 388 1013 LYD925 tomato|13v1|LEACS6 3891064 MGP7 sorghum|12v1|SB03G041200 391 1034 LGP1arabidopsis|10v1|AT1G32060 395 713 LGP3 arabidopsis|10v1|AT1G63680 396714 LGP6 arabidopsis|10v1|AT2G25080 397 715 LGP8arabidopsis|10v1|AT3G13720 398 716 LGP9 arabidopsis|10v1|AT3G17810 399717 LGP10 arabidopsis|10v1|AT3G20330 400 718 LGP12arabidopsis|10v1|AT3G54660 401 719 LGP18 arabidopsis|10v1|AT5G57030 402720 LGP19 b_juncea|10v2|E6ANDIZ01AHMLF 403 1067 LGP20barley|10v2|AV833857 404 1068 LGP21 barley|10v2|BG367409 405 723 LGP22barley|10v2|BI960336 406 724 LGP24 lettuce|10v1|AF321538 407 725 LGP25maize|10v1|AI622096 408 1069 LGP27 maize|10v1|BG360609 409 1070 LGP32tomato|11v1|AF030292 410 728 LGP34 tomato|11v1|BG131753 411 729 LGP35tomato|11v1|R27545 412 1071 LGP38 arabidopsis|10v1|AT2G15400 413 731LGP39 arabidopsis|10v1|AT2G15430 414 732 LGP41 sunflower|12v1|CD855665415 733 LGP42 tomato|11v1|BG128831 416 1072 LGP43 canola|11v1|EG019929417 735 LGP44 arabidopsis|10v1|AT5G37310 418 736 LGP45b_juncea|10v2|E6ANDIZ01A3IC5 419 737 LGP46 arabidopsis|10v1|AT5G58140420 738 LGP47 cotton|11v1|CO074926XX1 421 1073 LGP48canola|11v1|EG020435 422 1074 LGP49 canola|11v1|EE457807 423 741 LGP52sorghum|12v1|SB05G024560 424 742 LGP53 arabidopsis|10v1|AT5G45620 425743 LGP54 canola|11v1|AY518886 426 744 LGP58 cotton|11v1|BQ405024 4271075 LGP59 arabidopsis|10v1|AT3G06430 428 746 LGP60pigeonpea|11v1|SRR054580X101438 429 747 LGP61 sesame|12v1|SESI12V1412795430 748 LGP62 cephalotaxus|11v1|SRR064395X102206 431 749 LGP63rice|11v1|BI305215 432 750 LGP64 flaveria||11v1|SRR149229.109105 433 751LGP65 cotton|11v1|CO084001 434 752 LGP66 physcomitrella||10v1|BJ172182435 1076 LGP67 canola|11v1|DW997362 436 1077 LGP68 rice|11v1|AB042521437 755 LGP69 canola|11v1|EV020542 438 1078 LGP71 bean|12v1|CA896692 439757 LGP72 maize|10v1|AI967029 440 1079 LGP73 maize|10v1|AW054577 441 759LGP74 maize|10v1|BM075120 442 760 LGP75 maize|10v1|ZMU12233 443 761LGP76 rice|11v1|AU056832 444 762 LGP77 rice|11v1|BE040832 445 763 LGP78soybean|11v1|GLYMA04G40990 446 764 LGP79 soybean|11v1|GLYMA18G17600 4471080 LGP80 maize|10v1|BM500498 448 1081 LGP81 soybean|11v1|GLYMA09G02440449 767 LGP82 maize|10v1|AI964481 450 768 LGP83 barley|12v1|BE412944 451769 LGP84 bean|12v2|CA900203 452 1082 LGP85 bean|12v2|FE697169 453 1083LGP86 maize|10v1|AA979831 454 772 LGP87 maize|10v1|AI461460 455 773LGP88 maize|11v1|AI612489 456 1084 LGP89 maize|10v1|AI783343 457 1085LGP90 maize|10v1|AI855400 458 1086 LGP91 maize|10v1|AI943931 459 1087LGP94 maize|10v1|BE186218 460 780 LGP95 maize|10v1|BE511836 461 781LGP96 medicago||12v1|AI083076 462 1088 LGP97 medicago||12v1|AW687978 463783 LGP98 medicago||12v1|BE249345 464 784 LGP99 rice|11v1|AI978381 4651089 LGP100 rice|11v1|AU100980 466 786 LGP101 rice|11v1|BM038323 467 787LGP102 sorghum|12v1|SB01G004630 468 788 LGP103 sorghum|12v1|SB04G021670469 1090 LGP104 soybean|11v1|GLYMA05G04590 470 790 LGP105soybean|12v1|GLYMA11G31810 471 791 LGP106 soybean|13v2|BU577083 472 792LGP107 tomato|11v1|AW221249 473 793 LGP108 wheat|12v3|AL826289 474 1091LGP109 soybean|13v2|GLYMA16G02770T2 475 1092 LYD237arabidopsis|10v1|AT5G42190 477 797 MGP14 arabidopsis|10v1|AT5G42190 477797 LYD694 b_juncea|12v1|E6ANDIZ01A6E3M 489 809 LYD695b_juncea|12v1|E6ANDIZ01A8U9K 490 810 LYD696 b_juncea|12v1|E6ANDIZ01DJK4B491 1094 LYD698 b_rapa|11v1|CD812301 492 812 LYD699 b_rapa|11v1|CD815849493 813 LYD700 b_rapa|11v1|CD829408 494 814 LYD701 bean|12v1|CA913107495 815 LYD702 bean|12v2|AB020052 496 816 LYD703 bean|12v2|CA896596 497817 LYD704 bean|12v2|CA896633 498 818 LYD705 bean|12v2|CA896897 499 819LYD706 bean|12v2|CA896947 500 1095 LYD707 bean|12v2|CA897026 501 821LYD708 bean|12v2|CA897554 502 822 LYD710 bean|12v2|CA898557 503 823LYD711 bean|12v2|CA898580 504 1096 LYD713 bean|12v2|CA898845 505 825LYD714 bean|12v2|CA898855 506 826 LYD715 bean|12v2|CA899048 507 827LYD717 bean|12v2|CA899256 508 828 LYD718 bean|12v2|CA899264 509 1097LYD719 bean|12v2|CA899770 510 830 LYD720 bean|12v2|CA899773 511 831LYD721 bean|12v2|CA900278 512 1098 LYD722 bean|12v2|CA900376 513 1099LYD723 bean|12v2|CA900579 514 834 LYD725 bean|12v2|CA900816 515 1100LYD726 bean|12v2|CA901228 516 836 LYD727 bean|12v2|CA902441 517 837LYD729 bean|12v2|CA902538 518 838 LYD730 bean|12v2|CA905289 519 839LYD731 bean|12v2|CA905720 520 840 LYD733 bean|12v2|CA906136 521 841LYD735 bean|12v2|CA906321 522 842 LYD737 bean|12v2|CA908547 523 844LYD738 bean|12v2|CA909218 524 1101 LYD739 bean|12v2|CA909651 525 846LYD740 bean|12v2|CA910570 526 847 LYD741 bean|12v2|CA910581 527 848LYD742 bean|12v2|CA910778 528 1102 LYD744 bean|12v2|CA911083 529 1103LYD745 bean|12v2|CA911177 530 851 LYD746 bean|12v2|CA911180 531 852LYD747 bean|12v2|CA911414 532 853 LYD748 bean|12v2|CA911651 533 1104LYD749 bean|12v2|CA911692 534 855 LYD750 bean|12v2|CA911987 535 856LYD751 bean|12v2|CA911994 536 857 LYD752 bean|12v2|CA912567 537 858LYD753 bean|12v2|CA912688 538 1105 LYD754 bean|12v2|CA912714 539 860LYD755 bean|12v2|CA913041 540 861 LYD756 bean|12v2|CA913114 541 862LYD757 bean|12v2|CA913188 542 863 LYD758 bean|12v2|CA913400 543 1106LYD760 bean|12v2|CA913671 544 1107 LYD761 bean|12v2|CA913893 545 866LYD762 bean|12v2|CA915895 546 867 LYD763 bean|12v2|CA915968 547 1108LYD764 bean|12v2|CA916036 548 1109 LYD765 bean|12v2|CA916308 549 1110LYD767 bean|12v2|CA916492 550 871 LYD768 bean|12v2|CA916620 551 1111LYD769 bean|12v2|CB280523 552 873 LYD771 bean|12v2|CB539357 553 1112LYD772 bean|12v2|CB539439 554 1113 LYD773 bean|12v2|CB539539 555 876LYD774 bean|12v2|CB539605 556 877 LYD776 bean|12v2|CB540092 557 878LYD777 bean|12v2|CB540540 558 879 LYD778 bean|12v2|CB540751 559 1114LYD779 bean|12v2|CB540835 560 1115 LYD780 bean|12v2|CB540856 561 882LYD781 bean|12v2|CB541126 562 1116 LYD782 bean|12v2|CB541134 563 1117LYD783 bean|12v2|CB541623 564 885 LYD784 bean|12v2|CB542381 565 886LYD785 bean|12v2|CB542514 566 887 LYD786 bean|12v2|CB543395 567 888LYD788 bean|12v2|EG562919 568 889 LYD789 bean|12v2|EX303656 569 890LYD790 bean|12v2|EX304540 570 1118 LYD791 bean|12v2|EX304854 571 892LYD792 bean|12v2|EX304918 572 1119 LYD793 bean|12v2|EX305451 573 1120LYD794 bean|12v2|FE677973 574 895 LYD795 bean|12v2|FE683224 575 896LYD796 bean|12v2|FE684083 576 897 LYD798 bean|12v2|FE696773 577 1121LYD799 bean|12v2|FE707538 578 1122 LYD800 bean|12v2|FE708889 579 901LYD801 bean|12v2|FE897943 580 902 LYD802 bean|12v2|FE898020 581 903LYD803 bean|12v2|FE898128 582 904 LYD804 bean|12v2|FE898192 583 905LYD806 bean|12v2|FE898946 584 1123 LYD807 bean|12v2|FE898965 585 1124LYD809 bean|12v2|FE899199 586 908 LYD810 bean|12v2|FE899532 587 1125LYD811 bean|12v2|FE899588 588 1126 LYD812 bean|12v2|FG228526 589 911LYD813 bean|12v2|FG228626 590 1127 LYD814 bean|12v2|FG230712 591 1128LYD815 bean|12v2|FG231267 592 914 LYD816 bean|12v2|FG231286 593 1129LYD817 bean|12v2|HO778627 594 916 LYD818 bean|12v2|HO781301 595 1130LYD819 bean|12v2|HO783841 596 918 LYD821 bean|12v2|HO790120 597 919LYD823 bean|12v2|HO793451 598 921 LYD824 bean|12v2|HO799789 599 922LYD825 bean|12v2|HO806735 600 923 LYD826 bean|12v2|HO807062 601 924LYD828 bean|13v1|CA914375 602 1131 LYD829 bean|13v1|CB544235 603 1132LYD830 bean|13v1|FE690778 604 928 LYD831 canola|11v1|CN730435 605 929LYD833 canola|11v1|EE424371 606 930 LYD834 canola|11v1|EE482584 607 1133LYD835 cotton|11v1|AI055088 608 932 LYD836 cotton|11v1|AI729950 609 933LYD837 cotton|11v1|AY779339XX1 610 934 LYD838 cotton|11v1|BE052016XX1611 935 LYD839 cotton|11v1|BE055237 612 936 LYD840 cotton|11v1|BG444757613 937 LYD841 cotton|11v1|BM359931 614 1134 LYD842cotton|11v1|CB350435XX2 615 939 LYD843 cotton|11v1|CD485677 616 940LYD844 cotton|11v1|CO075283 617 1135 LYD845 cotton|11v1|CO085527XX2 6181136 LYD846 cotton|11v1|CO089064 619 1137 LYD847 cotton|11v1|CO112877XX1620 1138 LYD848 cotton|11v1|CO121493XX1 621 945 LYD849cotton|11v1|CO493081 622 1139 LYD850 cotton|11v1|DW500116 623 1140LYD851 medicago||12v1|AL386155 624 948 LYD852 medicago||12v1|AW256362625 1141 LYD853 medicago||12v1|AW683324 626 950 LYD854medicago||12v1|AW696146 627 951 LYD855 medicago||12v1|BE316923 628 952LYD856 medicago||12v1|BF643539 629 1142 LYD857 medicago||12v1|BF644247630 954 LYD858 rice|11v1|AA754378 631 955 LYD859 rice|13v2|BE228731 632956 LYD860 soybean|11v1|GLYMA13G44040 633 957 LYD861soybean|11v1|GLYMA15G01270 634 958 LYD863 soybean|12v1|GLYMA01G38410 635959 LYD864 soybean|12v1|GLYMA05G25960 636 960 LYD865soybean|12v1|GLYMA06G46850 637 1143 LYD866 soybean|12v1|GLYMA08G11220638 962 LYD867 soybean|12v1|GLYMA10G07340 639 963 LYD868soybean|12v1|GLYMA10G36220 640 1144 LYD870 soybean|12v1|GLYMA11G26980641 966 LYD871 soybean|12v1|GLYMA11G37390T2 642 967 LYD872soybean|12v1|GLYMA12G36480 643 968 LYD873 soybean|12v1|GLYMA14G09990 644969 LYD874 soybean|12v1|GLYMA14G37920 645 970 LYD876soybean|12v1|GLYMA17G07450 646 971 LYD877 soybean|12v1|GLYMA17G12750T4647 972 LYD878 soybean|12v1|GLYMA17G13780 648 973 LYD879soybean|12v1|GLYMA18G01820 649 974 LYD880 soybean|12v1|GLYMA18G01830 650975 LYD881 soybean|12v1|GLYMA18G48300 651 1145 LYD882soybean|12v1|GLYMA18G52810 652 977 LYD883 soybean|13v2|GLYMA01G44970 653978 LYD884 soybean|13v2|GLYMA02G40770 654 979 LYD886soybean|13v2|GLYMA11G20080 655 980 LYD887 soybean|13v2|GLYMA12G07990 656981 LYD888 soybean|13v2|GLYMA13G21490 657 982 LYD890soybean|13v2|GLYMA17G35060 658 983 LYD891 soybean|13v2|GLYMA19G40580 6591146 LYD892 tomato|11v1|AF096246 660 985 LYD893 tomato|11v1|AI486717 661986 LYD894 tomato|11v1|AI490031 662 987 LYD895 tomato|11v1|AI637290 663988 LYD896 tomato|11v1|AI771350 664 989 LYD897 tomato|11v1|AI773083 665990 LYD898 tomato|11v1|AI773883 666 991 LYD899 tomato|11v1|AI896477 6671147 LYD900 tomato|11v1|AW091881 668 1148 LYD901 tomato|11v1|AW217431669 994 LYD902 tomato|11v1|AW399640 670 995 LYD903 tomato|11v1|AW624231671 996 LYD904 tomato|11v1|BG123561 672 1149 LYD905 tomato|11v1|BG123981673 998 LYD906 tomato|11v1|BG125291 674 999 LYD907 tomato|11v1|BG125405675 1000 LYD908 tomato|11v1|BG127430 676 1150 LYD909tomato|11v1|BG128668 677 1002 LYD910 tomato|11v1|BG129449 678 1003LYD911 tomato|11v1|BG131325 679 1151 LYD912 tomato|11v1|BG132078 6801005 LYD913 tomato|11v1|BG132886 681 1006 LYD914 tomato|11v1|BG628916682 1007 LYD915 tomato|13v1|AI483969 683 1008 LYD917tomato|13v1|AI774553 684 1009 LYD918 tomato|13v1|AI776834 685 1010LYD919 tomato|13v1|AW160097 686 1011 LYD920 tomato|13v1|AW616349 6871012 LYD921 tomato|13v1|BG128290 688 1152 LYD922 tomato|13v1|BG133370689 1014 LYD923 tomato|13v1|BG627938 690 1153 LYD924tomato|13v1|BG735361 691 1016 LYD925 tomato|13v1|LEACS6 692 1017 LYD926bean|12v2|CA899181 693 1018 LYD929 bean|12v2|CA910968 694 1019 LYD930bean|12v2|CB542591 695 1020 LYD869_H1 soybean|13v2|GLYMA20G31360 6961021 MGP1 cotton|11v1|CO100059XX2 704 1029 MGP2arabidopsis|10v1|AT1G75950 705 1030 MGP4 soybean|12v1|GLYMA04G37510 7061031 MGP5 medicago||12v1|AL374833 707 1032 MGP7 sorghum|12v1|SB03G041200708 1034 MGP9 switchgrass|12v1|FL691989 709 1035 rice|13v2|BE041040_P11157 9276 cacao|13v1|CU618772_T1 1158 9277 sorghum|13v2|CD225902_P1 11599278 foxtail_millet|13v2|SRR350548X111147_P1 1160 9279brachypodium|13v2|BRADI2G04690_P1 1161 9280 rice|13v2|CB621206_P1 11629281 rice|13v2|AU225333_P1 1163 9282 maize|13v2|BQ703954_P1 3502 11276maize|13v2|BE056872_P1 3503 11277 chickpea|13v2|SRR133522.237740_P1 355111316 chickpea|13v2|SRR133517.100334_P1 3552 11317chickpea|13v2|SRR133517.103317_P1 3553 11318 rice|13v2|BI305582_P1 355411319 soybean|12v1|GLYMA09G33700T2 3555 11320soybean|13v2|GLYMA09G33700T2_P1 3556 11320 bean|13v1|SRR001335X371744_T13557 11321 bean|12v2|FE683652 3558 11322 bean|13v1|FE683652_P1 355911322 soybean|13v2|GLYMA05G31510_T1 3560 11323medicago||13v1|AW776098_P1 3561 11324 soybean|12v1|GLYMA18G19050 356211325 soybean|13v2|GLYMA18G19050_T1 3563 11325 bean|12v2|CK901542 356411326 bean|13v1|CK901542_T1 3565 11326 chickpea|13v2|SRR133517.106923_T13566 11327 peanut|13v1|SRR042418X140974_T1 3567 11328medicago||13v1|BE317701_T1 3568 11329 peanut|13v1|SRR042415X30056_T13569 11330 soybean|13v2|GLYMA12G01600_P1 3570 11331bean|13v1|CB280685_P1 3571 11332 peanut|13v1|EL966966_P1 3572 11333lupin||13v4|SRR520490.227669_P1 3573 11334lupin||13v4|SRR520490.212153_P1 3574 11335 medicago||13v1|AW256804_P13575 11336 soybean|13v2|GLYMA19G01910_P1 3576 11337bean|13v1|SRR001334X123668_P1 3577 11338nicotiana|_benthamiana|12v1|FG136526_P1 3578 11339nicotiana|_benthamiana|12v1|AJ719147_P1 3579 11340nicotiana|_benthamiana|12v1|BP748471_P1 3580 11341nicotiana|_benthamiana|12v1|EB424861_P1 3581 11342nicotiana|_benthamiana|12v1|FG173504_P1 3582 11342monkeyflower|12v1|DV211803_P1 3583 11343echinacea||13v1|EPURP13V11254457_P1 3584 11344triphysaria||13v1|EY004301_T1 3585 11345arabidopsis_lyrata|13v1|T21894_P1 3586 11346arabidopsis_lyrata|13v1|F15307_P1 3587 11347arabidopsis|13v2|AT1G64190_P1 3588 11348thellungiella_halophilum|13v1|BY804243_P1 3589 11349peanut|13v1|ES490969_P1 3590 11350 arabidopsis|13v2|AT5G41670_P1 359111351 ginseng|13v1|SRR547977.149183_T1 3592 11352 cacao|13v1|CU508968_P13593 11353 ginseng|13v1|SRR547977.32701_P1 3594 11354ginseng|13v1|HS077265_P1 3595 11355 soybean|13v2|GLYMA08G02410_P1 359611356 grape|13v1|GFXAM458581X1_P1 3597 11357soybean|13v2|GLYMA05G37170_P1 3598 11358 soybean|12v1|GLYMA05G37170 359911358 soybean|13v2|GLYMA05G37150_P1 3600 11358medicago||13v1|AL384701_P1 3601 11359thellungiella_halophilum|13v1|SRR487818.122950_P1 3602 11360prunus_mume|13v1|CB819193 3603 11361 poplar|13v1|BU829466_P1 3604 11362chickpea|13v2|GR912447_P1 3605 11363 ginseng|13v1|SRR547977.11969_T13606 11364 lupin||13v4|SRR520491.1010389_P1 3607 11365quinoa|13v2|SRR315568X203600_T1 3608 11366 poplar|13v1|AI165699_P1 360911367 bean|12v2|CA900025 3610 11368 bean|13v1|CA900025_P1 3611 11369bean|13v1|EX303864_T1 3612 11370 sorghum|13v2|AW679501_P1 8306 14914cenchrus||13v1|EB654709_P1 8307 14915 cenchrus||13v1|EB655983_P1 830814916 foxtail_millet|13v2|SRR350548X154353_P1 8309 14917switchgrass|12v1|FL975806 8310 14918 rice|13v2|AA751715_P1 8311 14919maize|13v2|AW506667_P1 8312 14920foxtail_millet|13v2|SRR350548X103395_P1 8313 14921maize|13v2|AW067342_P1 8314 14922 switchgrass|12v1|DN147336 8315 14923switchgrass|12v1|DN140971 8316 14924 brachypodium|13v2|BRADI1G26530_P18317 14925 rice|13v2|BI809972_P1 8318 14926 switchgrass|12v1|DN1419348319 14927 sorghum|13v2|CB926713_P1 8320 14928 rice|13v2|CA766993_P18321 14929 brachypodium|13v2|BRADI4G11300_T1 8322 14930maize|13v2|CF004751_P1 8323 14931foxtail_millet|13v2|SRR350548X193552_P1 8324 14932lolium||13v1|ERR246396S102853_T1 8325 14933foxtail_millet|13v2|SRR350548X158458_P1 8326 14934maize|13v2|AI677471_P1 8327 14935 rice|13v2|AF150113_P1 8328 14936sorghum|13v2|AW745516_P1 8329 14937 switchgrass|12v1|FE607135 8330 14938foxtail_millet|13v2|SRR350548X11557_P1 8331 14939lolium||13v1|ES699040_P1 8332 14940 brachypodium|13v2|BRADI4G04290_P18333 14941 cenchrus||13v1|SRR124128X153623D1_11 8334 14942echinacea||13v1|EPURP13V12373706_P1 8335 14943triphysaria||13v1|EY128870_P1 8336 14944 olea||13v1|SRR014463X19237D1_P18337 14945 basilicum||13v1|B10LEAF318589_P1 8338 14946cenchrus||13v1|SRR124128X217742D1_P1 8339 14947olea||13v1|SRR592583X111364D1_P1 8340 14948cenchrus||13v1|SRR124128X154700D1_P1 8341 14949monkeyflower|12v1|GO955392_P1 8342 14950nicotiana|_benthamiana|12v1|FS384845_P1 8343 14951grape|13v1|GSVIVT01024961001_P1 8344 14952quinoa|13v2|SRR315569X210009_P1 8345 14953 monkeyflower|12v1|DV209890_P18346 14954 ginseng|13v1|SRR547984.455348_P1 8347 14955quinoa|13v2|CQUI13V11038342_P1 8348 14956quinoa|13v2|SRR315570X375187_P1 8349 14956grape|13v1|GSVIVT01034172001_P1 8350 14957 prunus_mume|13v1|DY6476528351 14958 zostera||12v1|SRR057351X103123D1 8352 14959ginseng|13v1|PG13V1394312_P1 8353 14960 ginseng|13v1|SRR547977.21750_P18354 14961 ginseng|13v1|SRR547977.484054_P1 8355 14962nicotiana|_benthamiana|12v1|EB431713_P1 8356 14963nicotiana|_benthamiana|12v1|BP746194_P1 8357 14964ginseng|13v1|SRR547977.449157_P1 8358 14965 prunus_mume|13v1|CV0446158359 14966 centaurea||11v1|EH768661_T1 8360 14967fescue||13v1|HO060678_P1 8361 14968 ginseng|13v1|JK984156_P1 8362 14969tomato|13v1|BG125134_P1 8363 14970 echinacea||13v1|EPURP13V12056964_P18364 14971 centaurea||11v1|EH742119_P1 8365 14972lupin||13v4|SRR520491.1026789_P1 8366 14973 centaurea||11v1|EH721004_P18367 14972 soybean|12v1|GLYMA11G14830 8368 14974soybean|13v2|GLYMA11G14830_P1 8369 14974 soybean|12v1|GLYMA12G06770 837014975 soybean|13v2|GLYMA12G06770_P1 8371 14975lupin||13v4|SRR520491.101225_P1 8372 14976 chickpea|13v2|GR403089_P18373 14977 silicum|13v1|B10LEAF296739_P1 8374 14978switchgrass|12v1|FL891053 8375 14979 maize|13v2|AI973393_P1 8686 15224foxtail_millet|13v2|SRR350548X144392_P1 8687 15225sorghum|13v2|BG947008_T1 8688 15226 brachypodium|13v2|BRADI3G53290_P18689 15227 cenchrus||13v1|EB662826_P1 8690 15228sorghum|13v2|AW284830_P1 8928 15435foxtail_millet|13v2|SRR350548X142459_P1 8929 15436 rice|13v2|U37978_P18930 15437 brachypodium|13v2|BRADI2G04130_P1 8931 15438fescue||13v1|DT698307_P1 8932 15439 lolium||13v1|SRR029314X10387_P1 893315440 rice|13v2|AB060277_P1 8934 15441 sorghum|13v2|CD203908_P1 893515442 foxtail_millet|13v2|SRR350548X101163_P1 8936 15443maize|13v2|AI783320_P1 8937 15444 brachypodium|13v2|BRADI2G34470_P1 893815445 cenchrus||13v1|EB654978_T1 8939 15446 cacao|13v1|CU505404_P1 894015447 grape|13v1|GSVIVT01024573001_P1 8941 15448ginseng|13v1|SRR547977.146009_P1 8942 15449grape|13v1|GSVIVT01032677001_P1 8943 15450 ginseng|13v1|JK984772_P1 894415451 ginseng|13v1|SRR547977.113440_P1 8945 15452gossypium|_raimondii|13v1|BE054298_P1 8946 15453ginseng|13v1|SRR547986.158503_T1 8947 15454 sorghum|13v2|BM325215_P19272 15723 switchgrass|12v1|FL714538 9273 15724foxtail_millet|13v2|SRR350548X111433_P1 9274 15725sorghum|13v2|BM323764_P1 9275 15726 Table 1: Provided are the identifiedgenes, their annotation, organism and polynucleotide and polypeptidesequence identifiers. “polyn.” = polynucleotide; “polyp.” = polypeptide.

Example 2 Identification of Homologous (E.G., Orthologous) Sequencesthat Increase Yield, Fiber Yield, Fiber Quality, Growth Rate, Biomass,Oil Content, Vigor, ABST, and/or NUE of a Plant

The concepts of orthology and paralogy have recently been applied tofunctional characterizations and classifications on the scale ofwhole-genome comparisons. Orthologs and paralogs constitute two majortypes of homologs: The first evolved from a common ancestor byspecialization, and the latter are related by duplication events. It isassumed that paralogs arising from ancient duplication events are likelyto have diverged in function while true orthologs are more likely toretain identical function over evolutionary time.

To further investigate and identify putative orthologs of the genesaffecting plant yield, fiber yield, fiber quality, oil yield, oilcontent, seed yield, growth rate, vigor, biomass, abiotic stresstolerance, and fertilizer use efficiency (FUE) and/or nitrogen useefficiency of a plant, all sequences were aligned using the BLAST (BasicLocal Alignment Search Tool). Sequences sufficiently similar weretentatively grouped. These putative orthologs were further organizedunder a Phylogram—a branching diagram (tree) assumed to be arepresentation of the evolutionary relationships among the biologicaltaxa. Putative ortholog groups were analyzed as to their agreement withthe phylogram and in cases of disagreements these ortholog groups werebroken accordingly.

Expression data was analyzed and the EST libraries were classified usinga fixed vocabulary of custom terms such as developmental stages (e.g.,genes showing similar expression profile through development with upregulation at specific stage, such as at the seed filling stage) and/orplant organ (e.g., genes showing similar expression profile across theirorgans with up regulation at specific organs such as seed). Theannotations from all the ESTs clustered to a gene were analyzedstatistically by comparing their frequency in the cluster versus theirabundance in the database, allowing the construction of a numeric andgraphic expression profile of that gene, which is termed “digitalexpression”. The rationale of using these two complementary methods withmethods of phenotypic association studies of QTLs, SNPs and phenotypeexpression correlation is based on the assumption that true orthologsare likely to retain identical function over evolutionary time. Thesemethods provide different sets of indications on function similaritiesbetween two homologous genes, similarities in the sequencelevel—identical amino acids in the protein domains and similarity inexpression profiles.

The search and identification of homologous genes involves the screeningof sequence information available, for example, in public databases suchas the DNA Database of Japan (DDBJ), Genbank, and the European MolecularBiology Laboratory Nucleic Acid Sequence Database (EMBL) or versionsthereof or the MIPS database. A number of different search algorithmshave been developed, including but not limited to the suite of programsreferred to as BLAST programs. There are five implementations of BLAST,three designed for nucleotide sequence queries (BLASTN, BLASTX, andTBLASTX) and two designed for protein sequence queries (BLASTP andTBLASTN) (Coulson, Trends in Biotechnology: 76-80, 1994; Birren et al.,Genome Analysis, I: 543, 1997). Such methods involve alignment andcomparison of sequences. The BLAST algorithm calculates percent sequenceidentity and performs a statistical analysis of the similarity betweenthe two sequences. The software for performing BLAST analysis ispublicly available through the National Centre for BiotechnologyInformation. Other such software or algorithms are GAP, BESTFIT, FASTAand TFASTA. GAP uses the algorithm of Needleman and Wunsch (J. Mol.Biol. 48: 443-453, 1970) to find the alignment of two complete sequencesthat maximizes the number of matches and minimizes the number of gaps.

The homologous genes may belong to the same gene family. The analysis ofa gene family may be carried out using sequence similarity analysis. Toperform this analysis one may use standard programs for multiplealignments e.g. Clustal W. A neighbour-joining tree of the proteinshomologous to the genes in this invention may be used to provide anoverview of structural and ancestral relationships. Sequence identitymay be calculated using an alignment program as described above. It isexpected that other plants will carry a similar functional gene(ortholog) or a family of similar genes and those genes will provide thesame preferred phenotype as the genes presented here. Advantageously,these family members may be useful in the methods of the invention.Example of other plants are included here but not limited to, barley(Hordeum vulgare), Arabidopsis (Arabidopsis thaliana), maize (Zea mays),cotton (Gossypium), Oilseed rape (Brassica napus), Rice (Oryza sativa),Sugar cane (Saccharum officinarum), Sorghum (Sorghum bicolor), Soybean(Glycine max), Sunflower (Helianthus annuus), Tomato (Lycopersiconesculentum), Wheat (Triticum aestivum).

The above-mentioned analyses for sequence homology can be carried out ona full-length sequence, but may also be based on a comparison of certainregions such as conserved domains. The identification of such domains,would also be well within the realm of the person skilled in the art andwould involve, for example, a computer readable format of the nucleicacids of the present invention, the use of alignment software programsand the use of publicly available information on protein domains,conserved motifs and boxes. This information is available in the PRODOM(biochem (dot) ucl (dot) ac (dot) uk/bsm/dbbrowser/protocol/prodomqry(dot) html), PIR (pir (dot) Georgetown (dot) edu/) or Pfam (sanger (dot)ac (dot) uk/Software/Pfam/) database. Sequence analysis programsdesigned for motif searching may be used for identification offragments, regions and conserved domains as mentioned above. Preferredcomputer programs include, but are not limited to, MEME, SIGNALSCAN, andGENESCAN.

A person skilled in the art may use the homologous sequences providedherein to find similar sequences in other species and other organisms.Homologues of a protein encompass, peptides, oligopeptides,polypeptides, proteins and enzymes having amino acid substitutions,deletions and/or insertions relative to the unmodified protein inquestion and having similar biological and functional activity as theunmodified protein from which they are derived. To produce suchhomologues, amino acids of the protein may be replaced by other aminoacids having similar properties (conservative changes, such as similarhydrophobicity, hydrophilicity, antigenicity, propensity to form orbreak a-helical structures or 3-sheet structures). Conservativesubstitution tables are well known in the art (see for example Creighton(1984) Proteins. W.H. Freeman and Company). Homologues of a nucleic acidencompass nucleic acids having nucleotide substitutions, deletionsand/or insertions relative to the unmodified nucleic acid in questionand having similar biological and functional activity as the unmodifiednucleic acid from which they are derived.

Polynucleotides and polypeptides with significant homology to theidentified genes described in Table 1 (Example 1 above) were identifiedfrom the databases using BLAST software with the Blastp and tBlastnalgorithms as filters for the first stage, and the needle (EMBOSSpackage) or Frame+algorithm alignment for the second stage. Localidentity (Blast alignments) was defined with a very permissivecutoff—60% Identity on a span of 60% of the sequences lengths because itis used only as a filter for the global alignment stage. The defaultfiltering of the Blast package was not utilized (by setting theparameter “−F F”).

In the second stage, homologs were defined based on a global identity ofat least 80% to the core gene polypeptide sequence. Two distinct formsfor finding the optimal global alignment for protein or nucleotidesequences were used in this application:

1. Between two proteins (following the blastp filter):

EMBOSS-6.0.1 Needleman-Wunsch algorithm with the following modifiedparameters: gapopen=8 gapextend=2. The rest of the parameters wereunchanged from the default options described hereinabove.

2. Between a protein sequence and a nucleotide sequence (following thetblastn filter):

GenCore 6.0 OneModel application utilizing the Frame+algorithm with thefollowing parameters: model=frame+_p2n.model mode=qglobal-q=protein.sequence -db=nucleotide.sequence. The rest of the parametersare unchanged from the default options described hereinabove.

The query polypeptide sequences were the sequences listed in Table 1above, and the identified orthologous and homologous sequences having atleast 80% global sequence identity to said sequences are provided inTable 2, below. These homologous genes are expected to increase plantyield, seed yield, oil yield, oil content, growth rate, photosyntheticcapacity, fiber yield, fiber quality, biomass, vigor, ABST and/or NUE ofa plant.

Lengthy table referenced here US20160272987A1-20160922-T00001 Pleaserefer to the end of the specification for access instructions.

The output of the functional genomics approach described herein is a setof genes highly predicted to improve yield and/or other agronomicimportant traits such as growth rate, vigor, oil content, fiber yieldand/or quality, biomass, growth rate, abiotic stress tolerance, nitrogenuse efficiency, water use efficiency and fertilizer use efficiency of aplant by increasing their expression. Although each gene is predicted tohave its own impact, modifying the mode of expression of more than onegene is expected to provide an additive or synergistic effect on theplant yield and/or other agronomic important yields performance.Altering the expression of each gene described here alone or set ofgenes together increases the overall yield and/or other agronomicimportant traits, hence expects to increase agricultural productivity.

Example 3 Production of Barley Transcriptome and High ThroughputCorrelation Analysis Using 44K Barley Oligonucleotide Micro-Array

In order to produce a high throughput correlation analysis, the presentinventors utilized a Barley oligonucleotide micro-array, produced byAgilent Technologies [chem. (dot) agilent (dot) com/Scripts/PDS (dot)asp?1Page=50879]. The array oligonucleotide represents about 47,500Barley genes and transcripts. In order to define correlations betweenthe levels of RNA expression and yield or vigor related parameters,various plant characteristics of 25 different Barley accessions wereanalyzed. Among them, 13 accessions encompassing the observed variancewere selected for RNA expression analysis. The correlation between theRNA levels and the characterized parameters was analyzed using Pearsoncorrelation test [davidmlane (dot) com/hyperstat/A34739 (dot) html].

Experimental Procedures

Four tissues at different developmental stages [meristem, flower,booting spike, stem], representing different plant characteristics weresampled and RNA was extracted as described hereinabove under “GENERALEXPERIMENTAL AND BIOINFORMATICS METHODS”.

For convenience, each micro-array expression information tissue type hasreceived a Set ID as summarized in Table 3 below.

TABLE 3 Barley transcriptome expression sets Expression Set Set IDBooting spike at flowering stage under normal conditions 1 Floweringspike at flowering stage under normal conditions 2 Meristem at floweringstage under normal conditions 3 Stem at flowering stage under normalconditions 4 Table 3: Provided are the identification (ID) letters ofeach of the Barley expression sets.

Barley yield components and vigor related parameters assessment—13Barley accessions in 4 repetitive blocks (named A, B, C, and D), eachcontaining 4 plants per plot were grown at net house under normalconditions as recommended for commercial growth [normal growthconditions included irrigation given 2-3 times a week, and fertilizationgiven in the first 1.5 months of the growth period]; under low Nitrogen(80% percent less Nitrogen); or under drought stress (cycles of droughtand re-irrigating were conducted throughout the whole experiment,overall 40% less water were given in the drought treatment). Plants werephenotyped on a daily basis following the standard descriptor of barley(Table 4, below). Harvest was conducted while 50% of the spikes were dryto avoid spontaneous release of the seeds. Plants were separated to thevegetative part and spikes, of them, 5 spikes were threshed (grains wereseparated from the glumes) for additional grain analysis such as sizemeasurement, grain count per spike and grain yield per spike. Allmaterial was oven dried and the seeds were threshed manually from thespikes prior to measurement of the seed characteristics (weight andsize) using scanning and image analysis. The image analysis systemincluded a personal desktop computer (Intel P4 3.0 GHz processor) and apublic domain program—ImageJ 1.37 (Java based image processing program,which was developed at the U.S. National Institutes of Health and freelyavailable on the internet [rsbweb (dot) nih (dot) gov/]. Next, analyzeddata was saved to text files and processed using the JMP statisticalanalysis software (SAS institute).

TABLE 4 Barley standard descriptors Trait Parameter Range DescriptionGrowth habit Scoring 1-9 Prostrate (1) or Erect (9) Hairiness of ScoringP (Presence)/A Absence (1) or Presence (2) basal leaves (Absence) StemScoring 1-5 Green (1), Basal only or Half or more pigmentation (5) Daysto Days Days from sowing to emergence of Flowering awns Plant heightCentimeter (cm) Height from ground level to top of the longest spikeexcluding awns Spikes per plant Number Terminal Counting Spike lengthCentimeter (cm) Terminal Counting 5 spikes per plant Grains per spikeNumber Terminal Counting 5 spikes per plant Vegetative dry GramOven-dried for 48 hours at 70° C. weight Spikes dry Gram Oven-dried for48 hours at 30° C. weight Table 4

At the end of the experiment (50% of the spikes were dry) all spikesfrom plots within blocks A-D were collected, and the followingmeasurements were performed:

(i) Grains per spike—The total number of grains from 5 spikes that weremanually threshed was counted. The average grain per spike wascalculated by dividing the total grain number by the number of spikes.

(ii) Grain average size (cm)—The total grains from 5 spikes that weremanually threshed were scanned and images were analyzed using thedigital imaging system. Grain scanning was done using Brother scanner(model DCP-135), at the 200 dpi resolution and analyzed with Image Jsoftware. The average grain size was calculated by dividing the totalgrain size by the total grain number.

(iii) Grain average weight (mgr)—The total grains from 5 spikes thatwere manually threshed were counted and weight. The average weight wascalculated by dividing the total weight by the total grain number.

(iv) Grain yield per spike (gr) (=seed yield of 5 spikes)—The totalgrains from 5 spikes that were manually threshed were weight. The grainyield was calculated by dividing the total weight by the spike number.

(v) Spike length analysis—The five chosen spikes per plant were measuredusing measuring tape excluding the awns.

(vi) Spike number analysis—The spikes per plant were counted.

Additional parameters were measured as follows:

Growth habit scoring—At growth stage 10 (booting), each of the plantswas scored for its growth habit nature. The scale that was used was “1”for prostate nature till “9” for erect.

Hairiness of basal leaves—At growth stage 5 (leaf sheath strongly erect;end of tillering), each of the plants was scored for its hairinessnature of the leaf before the last. The scale that was used was “1” forprostate nature till “9” for erect.

Plant height—At harvest stage (50% of spikes were dry), each of theplants was measured for its height using measuring tape. Height wasmeasured from ground level to top of the longest spike excluding awns.

Days to flowering—Each of the plants was monitored for flowering date.Days of flowering was calculated from sowing date till flowering date.

Stem pigmentation—At growth stage 10 (booting), each of the plants wasscored for its stem color. The scale that was used was “1” for greentill “5” for full purple.

Vegetative dry weight and spike yield—At the end of the experiment (50%of the spikes were dry) all spikes and vegetative material from plotswithin blocks A-D were collected. The biomass and spikes weight of eachplot was separated, measured and divided by the number of plants.

Dry weight=total weight of the vegetative portion above ground(excluding roots) after drying at 70° C. in oven for 48 hours;

Spike yield per plant=total spike weight per plant (gr) after drying at30° C. in oven for 48 hours.

TABLE 5 Barley correlated parameters (vectors) Correlated parameter withCorrelation ID Grain weight [milligrams] 1 Grains size [mm²] 2 Grainsper spike [numbers] 3 Growth habit [scores 1-9] 4 Hairiness of basalleaves [scoring 1-2] 5 Plant height (cm) 6 Seed yield of 5 spikes[gr/spike] 7 Spike length [cm] 8 Spikes per plant [numbers] 9 Stempigmentation [scoring 1-5] 10 Vegetative dry weight [gram] 11 Days toflowering [days] 12 Table 5. Provided are the Barley correlatedparameters (vectors).

Experimental Results

13 different Barley accessions were grown and characterized for 12parameters as described above. The average for each of the measuredparameter was calculated using the JMP software and values aresummarized in Tables 6 and 7 below. Subsequent correlation analysisbetween the various transcriptome expression sets (Table 3) and theaverage parameters was conducted. Follow, results were integrated to thedatabase (Table 8 below).

TABLE 6 Measured parameters of correlation Ids in Barley accessionsEcotype/Treatment Line-1 Line-2 Line-3 Line-4 Line-5 Line-6 Line-7 135.05 28.06 28.76 17.87 41.22 29.73 25.22 2 0.27 0.23 0.24 0.17 0.290.28 0.22 3 20.23 17.98 17.27 17.73 14.47 16.78 12.12 4 2.60 2.00 1.923.17 4.33 2.69 3.60 5 1.53 1.33 1.69 1.08 1.42 1.69 1.30 6 134.27 130.50138.77 114.58 127.75 129.38 103.89 7 3.56 2.54 2.58 1.57 3.03 2.52 1.558 12.04 10.93 11.83 9.90 11.68 11.53 8.86 9 48.85 48.27 37.42 61.9233.27 41.69 40.00 10 1.13 2.50 1.69 1.75 2.33 2.31 1.70 11 78.87 66.1468.49 53.39 68.30 74.17 35.35 12 62.40 64.08 65.15 58.92 63.00 70.5452.80 Table 6. Provided are the values of each of the parametersmeasured in Barley accessions (1-7) according to the correlationidentifications (see Table 5).

TABLE 7 Barley accessions, additional measured parameters Ecotype/Treatment Line-8 Line-9 Line-10 Line-11 Line-12 Line-13 1 34.99 20.5827.50 37.13 29.56 19.58 2 0.28 0.19 0.22 0.27 0.27 0.18 3 14.07 21.5412.10 13.40 15.28 17.07 4 3.50 3.00 3.67 2.47 3.50 3.00 5 1.19 1.00 1.171.60 1.08 1.17 6 121.63 126.80 99.83 121.40 118.42 117.17 7 2.62 2.301.68 2.68 2.35 1.67 8 11.22 11.11 8.58 10.18 10.51 9.80 9 40.63 62.0049.33 50.60 43.09 51.40 10 2.19 2.30 1.83 3.07 1.58 2.17 11 58.33 62.2338.32 68.31 56.15 42.68 12 60.88 58.10 53.00 60.40 64.58 56.00 Providedare the values of each of the parameters measured in Barley accessions(8-13) according to the correlation identifications (see Table 5).

TABLE 8 Correlation between the expression level of the selectedpolynucleotides of the invention and their homologues in specifictissues or developmental stages and the phenotypic performance acrossBarley accessions Corr. Corr. Gene Exp. Set Gene Set Name R P value setID Name R P value Exp. set ID LGP22 0.82 3.46E−03 2 4 MGP3 0.74 8.95E−031 2 MGP3 0.71 1.42E−02 1 1 MGP3 0.78 5.01E−03 3 2 Provided are thecorrelations (R) and p-values (P) between the expression levels ofselected genes of some embodiments of the invention in various tissuesor developmental stages (Expression sets) and the phenotypic performancein various yield (seed yield, oil yield, oil content), biomass, growthrate and/or vigor components [Correlation (Corr.) vector (Vec.)Expression (Exp.)] Corr. Vector = correlation vector specified in Tables5, 6 and 7 Exp. Set = expression set specified in Table 3.

Example 4 Production of Barley Transcriptome and High ThroughputCorrelation Analysis Using 60K Barley Oligonucleotide Micro-Array

In order to produce a high throughput correlation analysis comparingbetween plant phenotype and gene expression level, the present inventorsutilized a Barley oligonucleotide micro-array, produced by AgilentTechnologies [chem. (dot) agilent (dot) com/Scripts/PDS (dot)asp?1Page=50879]. The array oligonucleotide represents about 60K Barleygenes and transcripts. In order to define correlations between thelevels of RNA expression and yield or vigor related parameters, variousplant characteristics of 15 different Barley accessions were analyzed.Among them, 10 accessions encompassing the observed variance wereselected for RNA expression analysis. The correlation between the RNAlevels and the characterized parameters was analyzed using Pearsoncorrelation test [davidmlane (dot) com/hyperstat/A34739 (dot) html].

Experimental Procedures

Analyzed Barley tissues—six tissues at different developmental stages[leaf, meristem, root tip, adventitious root, booting spike and stem],representing different plant characteristics, were sampled and RNA wasextracted as described above. Each micro-array expression informationtissue type has received a Set ID as summarized in Tables 9-11 below.

TABLE 9 Barley transcriptome expression sets (set 1) Expression Set SetID Root at vegetative stage under low N conditions 1 Root at vegetativestage under normal conditions 2 leaf at vegetative stage under low Nconditions 3 leaf at vegetative stage under normal conditions 4 root tipat vegetative stage under low N conditions 5 root tip at vegetativestage under normal conditions 6 Table 9. Provided are the expressionsets IDs at the vegetative stage.

TABLE 10 Barley transcriptome expression sets under normal and lownitrogen conditions (set 2) Expression Set Set ID Booting spike underlow nitrogen conditions 1 Booting spike under normal conditions 2 Leafunder low nitrogen conditions 3 Leaf under normal conditions 4 Stemunder low nitrogen conditions 5 Stem under normal conditions 6 Table 10.Provided are the barley transcriptome expression sets under normal andlow nitrogen conditions at the reproductive stage.

TABLE 11 Barley transcriptome expression sets under drought and recoveryconditions Expression Set Set ID booting spike at reproductive stageunder drought 1 conditions leaf at reproductive stage under droughtconditions 2 leaf at vegetative stage under drought conditions 3meristems at vegetative stage under drought conditions 4 root tip atvegetative stage under drought conditions 5 root tip at vegetative stageunder recovery drought 6 Table 11. Provided are the expression sets IDsat the reproductive and vegetative stages.

Barley yield components and vigor related parameters assessment—15Barley accessions in 5 repetitive blocks, each containing 5 plants perpot were grown at net house. Three different treatments were applied:plants were regularly fertilized and watered during plant growth untilharvesting as recommended for commercial growth under normal conditions[normal growth conditions included irrigation 2-3 times a week andfertilization given in the first 1.5 months of the growth period]; underlow Nitrogen (80% percent less Nitrogen); or under drought stress(cycles of drought and re-irrigating were conducted throughout the wholeexperiment, overall 40% less water as compared to normal conditions weregiven in the drought treatment). Plants were phenotyped on a daily basisfollowing the standard descriptor of barley (Tables 12 and 13, below).Harvest was conducted while all the spikes were dry. All material wasoven dried and the seeds were threshed manually from the spikes prior tomeasurement of the seed characteristics (weight and size) using scanningand image analysis. The image analysis system included a personaldesktop computer (Intel P4 3.0 GHz processor) and a public domainprogram—ImageJ 1.37 (Java based image processing program, which wasdeveloped at the U.S. National Institutes of Health and freely availableon the internet [rsbweb (dot) nih (dot) gov/]. Next, analyzed data wassaved to text files and processed using the JMP statistical analysissoftware (SAS institute).

Grains number—The total number of grains from all spikes that weremanually threshed was counted. Number of grains per plot was counted.

Grain weight (gr.)—At the end of the experiment all spikes of the potswere collected. The total grains from all spikes that were manuallythreshed were weighted. The grain yield was calculated by per plot.

Spike length and width analysis—At the end of the experiment the lengthand width of five chosen spikes per plant were measured using measuringtape excluding the awns.

Spike number analysis—The spikes per plant or per plot were counted.

Plant height—Each of the plants was measured for its height usingmeasuring tape. Height was measured from ground level to top of thelongest spike excluding awns at two time points at the Vegetative growth(30 days after sowing) and at harvest.

Spike weight—The biomass and spikes weight of each plot was separated,measured and divided by the number of plants.

Dry weight=total weight of the vegetative portion above ground(excluding roots) after drying at 70° C. in oven for 48 hours at twotime points at the Vegetative growth (30 days after sowing) and atharvest.

Root dry weight=total weight of the root portion underground afterdrying at 70° C. in oven for 48 hours at harvest.

Root/Shoot Ratio—The Root/Shoot Ratio was performed using Formula XXIIabove.

Total No of tillers—all tillers were counted per plot at two time pointsat the Vegetative growth (30 days after sowing) and at harvest.

SPAD—Chlorophyll content was determined using a Minolta SPAD 502chlorophyll meter and measurement was performed at time of flowering.SPAD meter readings were done on young fully developed leaf. Threemeasurements per leaf were taken per plot.

Root FW (gr.), root length (cm) and No. of lateral roots—3 plants perplot were selected for measurement of root fresh weight (FW), rootlength and for counting the number of lateral roots formed.

Shoot FW—weights of 3 plants per plot were recorded at differenttime-points.

Relative water content—Fresh weight (FW) of three leaves from threeplants each from different seed IDs was immediately recorded; thenleaves were soaked for 8 hours in distilled water at room temperature inthe dark, and the turgid weight (TW) was recorded. Total dry weight (DW)was recorded after drying the leaves at 60° C. to a constant weight.Relative water content (RWC) was calculated according to Formula Iabove.

Harvest Index (for barley)—The harvest index was performed using FormulaXVIII above.

Relative growth rate: the relative growth rate (RGR) of Plant Height(Formula III), SPAD (Formula IV) and number of tillers (Formula V) werecalculated according to the indicated Formulas described above.

TABLE 12 Barley correlated parameters (vectors) under low nitrogen andnormal conditions (set 1) Correlated parameter with Correlation IDLateral Roots (number) - Normal 1 Leaf Area (mm²) - Normal 2 LeafNumber - TP4 - Low N 3 Max Length (mm) - Normal 4 Max Width (mm) -Normal 5 Max Length (mm) - TP4 - Low N 6 Max Width (mm) - TP4 - Low N 7No of lateral roots - Low N - TP2 8 Num Leaves - Normal 9 Num Seeds -Normal 10 Num Spikes per plot - Normal 11 Num Tillers per plant - Normal12 Plant Height (cm) - TP1 - Normal 13 Plant Height (cm) - TP2 - Normal14 Plant Height (cm) - Low N - TP1 15 Plant Height (cm) - Low N - TP2 16Root FW (g) - Normal 17 Root Length (cm) - Normal 18 Root FW (g) - LowN - TP2 19 Root length (cm) - Low N - TP2 20 SPAD - Normal 21 SPAD - LowN - TP2 22 Seed Yield (gr) - Normal 23 Seed Number (per plot) - Low N 24Seed Yield (gr) - Low N 25 Shoot FW (g) - Normal 26 Spike Length (cm) -Normal 27 Spike Width (cm) - Normal 28 Spike weight per plot (g) -Normal 29 Spike Length (cm) - Low N 30 Spike Width (cm) - Low N 31 Spiketotal weight (per plot) - Low N 32 Total Tillers per plot (number) -Normal 33 Total Leaf Area (mm²) - TP4 - Low N 34 Total No of Spikes perplot - Low N 35 Total No of tillers per plot - Low N 36 shoot FW (gr) -Low N - TP2 37 Table 12. Provided are the barley correlated parameters.TP = time point; DW = dry weight; FW = fresh weight; Low N = LowNitrogen.

TABLE 13 Barley correlated parameters (vectors) for maintenance ofperformance under normal conditions (set 2) Correlated parameter withCorrelation ID Grain Perimeter (mm) 1 Grain area (cm²) 2 Grain length(mm) 3 Grain width (mm) 4 Grains DW/Shoots DW (ratio) 5 Grains per plot(number) 6 Grains weight per plant (gr) 7 Grains weight per plot (gr) 8Plant Height (cm) 9 Roots DW (gr) 10 Row number (number) 11 Spikes FW(Harvest) (gr) 12 Spikes num (number) 13 Tillering (Harvest) (number) 14Vegetative DW (Harvest) (gr) 15 percent of reproductive tillers (%) 16shoot/root ratio (ratio) 17 Table 13. Provided are the barley correlatedparameters. ““DW” = dry weight; “ratio” - maintenance of phenotypicperformance under drought in comparison to normal conditions.

TABLE 14 Barley correlated parameters (vectors) under drought conditionsCorrelated parameter with Correlation ID Chlorophyll levels 1 Dry weightharvest (gr.) 2 Dry weight vegetative growth (gr.) 3 Fresh weight (gr.)4 Grain number 5 Grain weight (gr.) 6 Harvest index 7 Heading date 8Height Relative growth rate 9 Number of tillers Relative growth rate 10Plant height T1 (cm) 11 Plant height T2 (cm) 12 RBiH/BiH (root/shootratio, Formula XXII hereinabove) 13 Relative water content 14 Root dryweight (gr.) 15 Root fresh weight (gr.) 16 Root length (cm) 17 SPADRelative growth rate 18 Spike length (cm) 19 Spike number per plant 20Spike weight per plant (gr.) 21 Spike width (cm) 22 Tillers number T1(number) 23 Tillers number T2 (number) 24 Lateral root number (number)25 Table 14. Provided are the barley correlated parameters. “TP” = timepoint; “DW” = dry weight; “FW” = fresh weight; “Low N” = Low Nitrogen;“Normal” = regular growth conditions. “Max” = maximum.

TABLE 15 Barley correlated parameters (vectors) for maintenance ofperformance under drought conditions Correlated parameter withCorrelation ID Chlorophyll levels ratio 1 Dry weight at harvest ratio 2Dry weight_vegetative growth ratio 3 Fresh weight ratio 4 Grain numberratio 5 Grain weight ratio 6 Harvest index ratio 7 Heading date ratio 8Plant height ratio 9 Root/shoot ratio 10 Relative water content ratio 11Root dry weight ratio 12 Root fresh weight ratio 13 Root length ratio 14Spike length ratio 15 Spike number ratio 16 Spike weight per plant ratio17 Spike width ratio 18 Tillers number ratio 19 lateral root numberratio 20 Table 15. Provided are the barley correlated parameters. ““DW”= dry weight; “ratio” - maintenance of phenotypic performance underdrought in comparison to normal conditions.

Experimental Results

15 different Barley accessions were grown and characterized fordifferent parameters as described above. The average for each of themeasured parameter was calculated using the JMP software and values aresummarized in Tables 16-24 below. Subsequent correlation analysisbetween the various transcriptome sets and the average parameters wasconducted (Tables 25-28). Follow, results were integrated to thedatabase.

TABLE 16 Measured parameters of correlation IDs in Barley accessions(set 1) Ecotype/ Treatment Line-1 Line-2 Line-3 Line-4 Line-5 Line-6Line-7 Line-8 Line-9 Line-10 3 8.00 8.00 7.50 8.50 10.00 11.50 8.60 6.337.50 10.00 6 102.90 107.78 111.57 142.42 152.38 149.33 124.08 95.00124.12 135.17 7 5.25 5.17 5.12 5.30 5.20 5.33 5.32 5.10 5.15 5.10 8 5.006.00 4.33 6.00 6.33 6.00 6.67 4.67 5.67 7.33 15 41.00 82.00 61.40 59.4065.80 47.80 53.80 56.40 81.80 44.60 16 16.33 18.83 17.33 26.00 22.5018.17 19.67 19.83 19.17 19.17 19 0.38 0.23 0.12 0.40 0.88 0.50 0.43 0.320.30 0.55 20 24.67 21.67 22.00 21.67 22.17 23.00 30.50 22.83 23.83 24.5022 24.03 23.30 26.47 23.90 26.63 23.20 25.43 24.23 25.03 26.07 24 230.20164.60 88.25 133.60 106.00 222.60 219.20 143.45 201.80 125.00 25 9.767.31 3.30 5.06 6.02 9.74 7.35 5.80 7.83 6.29 30 15.19 19.61 16.30 19.3290.22 16.44 20.44 18.84 18.77 16.65 31 7.95 8.13 9.43 4.94 9.60 7.167.06 8.51 10.01 9.40 32 13.74 13.44 9.15 11.64 11.34 15.06 12.18 10.9512.18 10.62 34 39.40 46.27 51.51 57.07 67.78 64.15 52.42 46.15 68.0257.91 35 12.20 9.00 11.60 25.00 7.80 14.50 15.00 7.00 5.40 8.40 36 16.2014.60 16.00 20.75 12.50 18.80 21.20 11.00 6.75 14.00 37 0.43 0.43 0.330.58 0.78 0.53 0.45 0.43 0.50 0.62 1 7.00 8.67 8.33 9.67 10.70 9.67 9.678.67 10.00 9.67 2 294.00 199.00 273.00 276.00 313.00 309.00 259.00291.00 299.00 296.00 4 502.00 348.00 499.00 594.00 535.00 551.00 479.00399.00 384.00 470.00 5 5.77 5.45 5.80 6.03 4.63 5.33 5.83 5.43 5.75 6.039 24.20 18.20 22.70 25.50 23.20 28.30 22.20 19.00 17.30 22.00 10 1090.00510.00 242.00 582.00 621.00 1070.00 903.00 950.00 984.00 768.00 11 41.5032.00 36.00 71.40 34.20 45.60 49.80 28.00 19.30 38.00 12 2.00 2.00 1.002.33 2.33 3.33 2.33 1.33 1.33 1.67 13 39.20 37.00 36.80 49.80 46.8034.80 43.20 35.70 46.20 40.20 14 64.70 84.00 67.40 82.00 72.00 56.6065.80 62.80 91.60 66.20 17 0.27 0.27 0.25 0.35 0.62 0.27 0.35 0.32 0.230.27 18 21.30 15.00 21.80 20.30 27.20 16.00 24.00 13.50 21.50 15.20 2139.10 41.40 35.20 33.70 34.20 42.80 37.00 36.90 35.00 36.80 23 46.4019.80 10.80 22.60 30.30 54.10 37.00 42.00 35.40 38.30 26 2.17 1.90 1.253.00 15.60 3.02 2.58 1.75 2.18 1.82 27 16.50 19.20 18.30 20.40 17.2019.10 20.30 21.70 16.50 16.10 28 9.54 9.05 8.25 6.55 10.50 8.83 7.3810.40 10.20 10.30 29 69.40 39.40 34.90 50.30 60.80 79.10 62.70 60.0055.90 59.70 33 46.70 41.60 40.00 48.80 34.60 48.60 49.20 29.00 27.5038.80

TABLE 17 Measured parameters of correlation IDs in Barley accessionsunder normal conditions (set 2) Ecotype/ Treatment Line-1 Line-2 Line-3Line-4 Line-5 Line-6 Line-7 Line-8 1 2.24 2.24 2.18 2.05 2.08 2.03 2.251.88 2 0.25 0.24 0.24 0.23 0.24 0.25 0.24 0.22 3 0.89 0.87 0.86 0.800.82 0.78 0.90 0.72 4 0.35 0.35 0.35 0.37 0.37 0.41 0.35 0.39 5 0.400.16 1.01 0.79 0.41 0.99 0.66 0.61 6 683.40 510.50 1093.50 767.60 621.001069.00 987.75 903.20 7 6.65 3.96 9.27 7.65 6.06 10.83 7.94 7.40 8 33.2419.81 46.37 38.25 30.30 54.13 39.69 36.98 9 76.40 84.00 64.67 66.2072.00 56.60 68.00 65.80 10 118.30 150.68 86.28 85.19 120.31 90.70 40.5890.51 11 6.00 6.00 6.00 6.00 6.00 2.80 6.00 2.00 12 69.84 39.86 69.4059.72 60.83 79.12 63.50 62.74 13 38.60 32.00 41.50 38.00 34.20 45.6030.00 49.80 14 44.25 41.60 46.67 38.80 34.60 48.60 32.40 55.20 15 89.2099.65 45.79 49.39 74.32 55.11 47.29 60.32 16 82.30 77.75 86.69 94.2389.74 93.73 89.49 90.27 17 1.48 0.64 0.84 0.82 1.15 0.69 1.26 0.72Provided are the values of each of the parameters (as described above)measured in Barley accessions (line) under normal growth conditions.Growth conditions are specified in the experimental procedure section.

TABLE 18 Additional measured parameters of correlation IDs in Barleyaccessions under normal conditions (set 2) Eco- type/ Treat- Line- Line-Line- Line- Line- Line- Line- ment 9 10 11 12 13 14 15 1 2.09 2.03 2.021.98 1.69 1.98 1.89 2 0.23 0.22 0.23 0.21 0.18 0.19 0.17 3 0.82 0.790.80 0.80 0.65 0.82 0.77 4 0.36 0.36 0.37 0.34 0.35 0.29 0.29 5 0.281.04 0.12 0.86 0.58 0.05 0.08 6 581.80 904.40 242.40 928.40 984.20157.67 263.25 7 4.52 8.41 2.00 8.05 7.07 0.75 1.14 8 22.58 39.68 10.8440.26 35.37 3.73 5.68 9 82.00 62.80 67.40 76.20 91.60 44.00 52.75 1092.59 63.95 286.63 95.79 34.04 121.27 206.75 11 2.00 5.20 6.00 6.00 6.004.67 4.00 12 50.30 59.95 34.92 60.08 55.88 16.93 21.70 13 71.40 28.0036.00 27.60 23.60 54.67 48.00 14 50.60 29.00 40.00 28.50 27.50 26.00 1588.01 38.89 97.71 48.33 62.52 57.97 72.78 16 91.21 92.50 91.73 85.31 171.17 0.71 0.38 0.51 2.16 0.67 0.39 Provided are the values of each ofthe parameters (as described above) measured in Barley accessions (line)under normal growth conditions. Growth conditions are specified in theexperimental procedure section.

TABLE 19 Measured parameters of correlation IDs in Barley accessionsunder low nitrogen conditions (set 2) Ecotype/ Treatment Line-1 Line-2Line-3 Line-4 Line-5 Line-6 Line-7 Line-8 1 2.28 2.33 2.28 2.08 2.131.96 2.09 1.88 2 0.25 0.25 0.25 0.24 0.25 0.23 0.23 0.21 3 0.90 0.920.93 0.82 0.86 0.76 0.83 0.73 4 0.35 0.35 0.35 0.36 0.37 0.38 0.35 0.365 0.39 0.42 1.25 0.69 0.43 0.87 0.77 0.53 6 153.20 164.60 230.20 125.00100.00 222.60 159.40 219.20 7 1.34 1.46 1.95 1.26 1.13 1.95 1.28 1.47 86.68 7.31 9.76 6.29 5.67 9.74 6.40 7.35 9 75.20 82.00 41.00 44.60 65.8047.80 60.60 53.80 10 39.91 26.24 17.31 32.91 33.87 83.84 29.65 37.21 116.00 6.00 6.00 6.00 6.00 2.00 6.00 2.00 12 11.40 13.44 13.74 10.62 11.3415.06 11.64 12.18 13 10.80 9.00 12.20 8.40 7.80 14.50 8.40 15.00 1416.00 14.60 16.20 14.00 12.50 18.80 11.60 21.20 15 17.42 17.76 8.25 7.2813.25 11.32 8.95 14.18 16 68.68 61.85 76.94 59.63 65.63 79.84 73.8571.01 17 0.69 1.08 0.77 0.38 0.83 0.42 0.28 0.57 Provided are the valuesof each of the parameters (as described above) measured in Barleyaccessions (line) under low N growth conditions. Growth conditions arespecified in the experimental procedure section.

TABLE 20 Additional measured parameters of correlation IDs in Barleyaccessions under low nitrogen conditions (set 2) Eco- type/ Treat- Line-Line- Line- Line- Line- Line- Line- ment 9 10 11 12 13 14 15 1 2.19 1.882.03 2.11 1.77 2.00 1.90 2 0.23 0.20 0.22 0.23 0.19 0.19 0.17 3 0.860.73 0.81 0.85 0.68 0.81 0.79 4 0.35 0.35 0.35 0.35 0.36 0.29 0.27 50.34 0.87 0.15 0.58 0.76 0.05 0.07 6 133.60 134.40 88.25 174.25 201.8086.67 61.60 7 0.98 1.16 0.92 1.33 1.57 0.29 0.22 8 5.06 5.43 4.62 6.677.83 1.44 1.12 9 59.40 56.40 61.40 65.60 81.80 69.00 57.40 10 44.3814.46 41.54 23.75 20.87 49.69 54.02 11 2.00 5.20 6.00 6.00 6.00 2.002.00 12 11.64 8.76 9.15 12.42 12.18 5.68 5.04 13 25.00 7.00 11.60 7.605.40 16.40 12.00 14 23.50 11.00 16.00 10.75 6.75 35.00 15 15.68 6.4255.92 11.54 10.88 58.92 17.05 16 95.83 64.87 68.75 74.24 81.40 37.14 170.60 0.55 2.88 1.36 0.89 2.49 0.40 Provided are the values of each ofthe parameters (as described above) measured in Barley accessions (line)under low N growth conditions. Growth conditions are specified in theexperimental procedure section.

TABLE 21 Measured parameters of correlation IDs in Barley accessions(1-8) under drought and recovery conditions Ecotype/ Treatment Line-1Line-2 Line-3 Line-4 Line-5 Line-6 Line-7 Line-8 1 41.33 33.57 36.5740.50 45.07 39.73 38.33 36.17 2 6.15 5.05 3.20 3.28 4.76 3.55 4.52 3.383 0.21 0.21 0.17 4 1.90 1.52 1.17 1.95 1.90 1.22 1.75 1.58 5 170.00267.50 111.00 205.33 153.60 252.50 288.40 274.50 6 5.55 9.80 3.55 7.205.28 7.75 9.92 10.25 7 0.47 0.66 0.53 0.69 0.53 0.69 0.69 0.75 8 75.0071.00 65.00 66.75 90.00 90.00 9 0.27 0.86 0.73 0.88 0.40 0.94 0.70 0.7110 0.07 0.10 0.06 0.07 0.16 0.06 0.10 0.05 11 33.33 27.00 31.33 34.1731.33 30.33 28.67 38.67 12 46.00 52.80 35.00 38.00 45.20 48.00 37.6741.20 13 0.01 0.01 0.01 0.01 0.03 0.02 0.01 0.01 14 80.60 53.40 55.8743.21 69.78 45.49 76.51 15 77.52 60.19 27.13 18.62 117.42 70.72 37.3425.56 16 2.07 1.48 1.12 1.87 1.67 1.68 1.62 0.85 17 21.67 20.33 22.0024.00 20.67 18.33 21.00 20.33 18 0.09 −0.12 0.00 0.01 0.04 −0.07 0.010.00 19 16.70 16.85 13.27 13.55 14.19 15.64 15.66 17.49 20 4.20 4.367.60 8.44 4.92 3.43 6.90 5.80 21 17.72 24.24 18.20 18.00 19.50 15.0023.40 28.16 22 8.64 9.07 7.82 7.32 8.74 7.62 6.98 8.05 23 2.00 2.00 1.671.67 2.00 1.67 2.33 1.00 24 11.68 9.04 10.92 10.16 10.32 8.78 13.00 7.4425 8.33 8.67 7.33 7.67 6.67 6.67 7.67 6.67

TABLE 22 Measured parameters of correlation IDs in Barley accessionsunder drought and recovery conditions additional lines (9-15) Eco- type/Treat- Line- Line- Line- Line- Line- Line- Line- ment 9 10 11 12 13 1415  1 42.13 31.77 33.47 42.37 42.27 36.77 40.63  2 5.67 3.31 2.65 5.126.86 3.11 3.74  3 0.25 0.13 0.19 0.22  4 1.88 1.73 1.00 0.90 0.90 1.430.83  5 348.50 358.00 521.39 71.50 160.13 376.67 105.00  6 8.50 14.0317.52 2.05 5.38 11.00 2.56  7 0.60 0.81 0.87 0.29 0.44 0.78 0.41  890.00 90.00 81.60 90.00  9 0.77 0.80 0.92 0.39 0.88 −0.13 0.20 10 0.100.06 0.06 0.18 0.15 0.02 0.44 11 33.67 28.43 27.50 25.00 27.00 31.0022.33 12 40.80 49.86 43.00 47.40 64.80 52.60 32.00 13 0.01 0.01 0.020.02 0.01 0.01 0.03 14 87.41 58.32 80.58 73.09 15 66.18 22.13 41.12116.95 84.10 37.46 98.86 16 1.45 1.38 0.82 0.58 0.63 1.07 0.70 17 21.6719.67 16.67 17.00 15.17 27.00 15.00 18 −0.06 0.04 0.05 0.00 −0.07 0.03−0.06 19 16.00 18.31 17.42 14.23 14.81 16.54 12.72 20 8.55 9.67 5.423.05 4.07 3.72 3.21 21 21.96 33.03 34.80 11.73 18.78 21.00 9.88 22 6.066.73 9.55 7.84 7.81 8.35 5.47 23 2.33 3.00 1.00 1.00 1.00 1.00 1.00 2413.92 11.00 6.78 8.45 9.15 5.12 16.13 25 6.00 8.67 7.67 6.33 7.00 7.006.67

TABLE 23 Measured parameters of correlation IDs in Barley accessions formaintenance of performance under drought conditions Ecotype/ TreatmentLine-1 Line-2 Line-3 Line-4 Line-5 Line-6 Line-7 Line-8 1 0.98 0.72 1.31.06 1.03 0.95 0.82 0.93 2 0.61 0.45 0.59 0.67 0.41 0.54 0.75 0.65 30.93 0.71 0 0 0 0.65 0 0.92 4 0.6 0.5 0.47 0.68 0.46 0.47 0.58 0.62 50.12 0.22 0.11 0.19 0.17 0.21 0.22 0.24 6 0.08 0.17 0.06 0.14 0.15 0.140.15 0.2 7 0.54 0.79 0.58 0.75 0.7 0.77 0.75 0.83 8 0 1.12 1.3 0 1 1.061.37 1.22 9 0.51 0.61 0.67 0.72 0.61 0.59 0.7 0.63 9 0.51 0.61 0.67 0.720.61 0.59 0.7 0.63 10 1.55 0.97 1.12 0.56 1.72 1.97 0.67 0.96 11 0.780.58 0.9 0 0.65 0.56 0.78 0.83 12 0.94 0.44 0.66 0.37 0.71 1.06 0.5 0.6213 1.1 1 1.02 1.67 0.8 0.81 1.13 0.34 14 0.66 0.74 1.16 0.78 0.76 0.760.68 0.77 15 0.83 0.82 0.86 0.77 0.78 0.94 0.83 0.89 16 0.73 0.96 1.111.3 0.83 0.62 0.87 1.12 17 0.16 0.23 0.19 0.23 0.25 0.18 0.23 0.34 180.75 0.77 0.68 0.67 0.87 0.66 0.75 0.74 19 1.87 1.57 1.72 1.8 1.6 1.611.63 1.59 19 1.87 1.57 1.72 1.8 1.6 1.61 1.63 1.59 20 1.09 0.74 0.790.88 0.71 0.65 0.85 0.77 Provided are the values of each of theparameters (as described above) measured in Barley accessions (line) formaintenance of performance under drought (calculated as % of changeunder drought vs normal growth conditions). Growth conditions arespecified in the experimental procedure section.

TABLE 24 Additional measured parameters of correlation IDs in Barleyaccessions for maintenance of performance under drought conditionsEcotype/ Line- Line- Line- Line- Line- Line- Line- Treatment 9 10 11 1213 14 15 1 0.93 0.8 0.94 0.96 1.01 0.93 1.03 2 0.77 0.8 0.68 0.42 0.650.52 0.46 3 1.01 0 0 0.94 0 0.7 0 4 0.74 0.81 0.72 0.37 0.4 5 0.25 0.580.43 0.1 0.1 0.28 0.43 6 0.14 0.47 0.32 0.07 0.07 0.2 0.32 7 0.67 0.920.93 0.41 0.5 0.87 0.82 8 0 1.2 1 9 0.66 0.87 0.86 0.64 0.79 0.56 0.51 90.66 0.87 0.86 0.64 0.79 0.56 0.51 10 1.14 1.08 1.38 1.84 1.31 2.06 1.4611 0.5 0 0 0.78 0.55 12 0.88 0.87 0.94 0.77 0.85 1.06 0.68 13 0.85 0.580.07 1.06 0.3 0.44 0.93 14 1.12 0.56 0.42 0.82 0.43 0.71 0.8 15 0.780.94 0.88 0.77 0.86 0.97 0.78 16 1.09 1.09 0.92 0.49 0.65 0.99 0.52 170.22 0.68 0.55 0.18 0.18 0.27 0.25 18 0.74 0.86 0.85 0.79 0.72 0.72 0.8819 1.75 1.33 1.62 1.33 1.4 1.22 1.96 19 1.75 1.33 1.62 1.33 1.4 1.221.96 20 0.58 0.96 0.88 0.95 0.78 0.66 0.87 Provided are the values ofeach of the parameters (as described above) measured in Barleyaccessions (line) for maintenance of performance under drought(calculated as % of change under drought vs normal growth conditions).Growth conditions are specified in the experimental procedure section.

TABLE 25 Correlation between the expression level of selected genes ofsome embodiments of the invention in various tissues and the phenotypicperformance under low nitrogen, normal or drought stress conditionsacross Barley accessions (set 1) Gene Exp. Corr. Gene Exp. Corr. Name RP value set Set ID Name R P value set Set ID LGP20 0.74 1.42E−02 5 30LGP20 0.90 4.15E−04 5 19 LGP20 0.74 1.43E−02 5 3 LGP20 0.76 1.00E−02 537 LGP20 0.71 2.05E−02 5 6 LGP21 0.81 1.49E−02 6 17 LGP21 0.85 7.00E−034 21 LGP21 0.76 1.74E−02 2 18 LGP21 0.92 4.54E−04 2 26 LGP21 0.853.81E−03 2 17 LGP21 0.82 7.25E−03 3 19 LGP21 0.86 3.15E−03 3 3 LGP210.86 2.94E−03 3 37 LGP21 0.76 1.73E−02 3 6 LGP22 0.74 3.60E−02 6 33LGP22 0.78 2.17E−02 6 12 LGP22 0.72 1.85E−02 5 32 LGP22 0.75 2.00E−02 226 LGP83 0.75 2.11E−02 3 32 MGP3 0.80 1.80E−02 6 21 MGP3 0.78 2.14E−02 612 MGP3 0.72 2.86E−02 3 7 MGP3 0.72 2.81E−02 3 35 Provided are thecorrelations (R) between the expression levels yield improving genes andtheir homologs in various tissues [Expression (Exp) sets] and thephenotypic performance [yield, biomass, growth rate and/or vigorcomponents (Correlation vector (Corr.))] under normal, low nitrogen anddrought conditions across barley varieties. P = p value.

TABLE 26 Correlation between the expression level of selected genes ofsome embodiments of the invention in various tissues and the phenotypicperformance under low nitrogen and normal growth conditions acrossBarley accessions (set 2) Gene Exp. Corr. Gene Exp. Corr. Name R P valueset Set ID Name R P value set Set ID LGP22 0.75 1.32E−02 5 15 MGP3 0.702.33E−02 2 11 MGP3 0.73 1.65E−02 3 9 MGP3 0.81 4.46E−03 6 11 MGP3 0.861.29E−03 5 17 MGP3 0.71 2.02E−02 4 5 MGP3 0.79 6.70E−03 4 11 MGP3 0.921.99E−04 1 17 Correlations (R) between the genes expression levels invarious tissues and the phenotypic performance. “Corr. ID”—correlationset ID according to the correlated parameters Table above. “Exp.Set”—Expression set. “R” = Pearson correlation coefficient; “P” = pvalue.

TABLE 27 Correlation between the expression level of selected genes ofsome embodiments of the invention in various tissues and the phenotypicperformance under drought stress conditions across Barley accessionsGene Exp. Corr. Gene Exp. Corr. Name R P value set Set ID Name R P valueset Set ID LGP20 0.73 9.89E−02 1 11 LGP20 0.78 2.31E−02 3 20 LGP20 0.753.21E−02 5 23 LGP20 0.83 4.21E−02 5 8 LGP20 0.86 2.70E−03 4 20 LGP200.82 6.90E−03 4 23 LGP21 0.80 5.74E−02 1 10 LGP21 0.72 1.04E−01 1 9LGP21 0.73 6.35E−02 2 25 LGP21 0.77 1.44E−02 4 20 LGP21 0.74 2.36E−02 418 LGP22 0.73 1.03E−01 1 19 LGP22 0.83 1.12E−02 3 22 LGP22 0.75 3.54E−025 23 LGP22 0.80 9.95E−03 4 20 LGP22 0.75 2.08E−02 4 23 LGP22 0.713.20E−02 4 24 LGP83 0.73 1.03E−01 1 22 LGP83 0.75 8.58E−02 1 18 LGP830.71 4.89E−02 3 13 LGP83 0.71 7.35E−02 2 17 LGP83 0.83 1.96E−02 2 11LGP83 0.79 2.01E−02 5 19 MGP3 0.77 7.54E−02 1 7 MGP3 0.82 4.43E−02 1 12MGP3 0.85 3.21E−02 1 25 MGP3 0.74 9.14E−02 1 6 MGP3 0.74 9.23E−02 1 21MGP3 0.83 1.04E−02 3 20 MGP3 0.85 7.17E−03 3 12 MGP3 0.80 9.31E−03 6 19MGP3 0.80 1.02E−02 6 2 MGP3 0.74 2.38E−02 6 15 MGP3 0.78 3.89E−02 2 22MGP3 0.78 3.67E−02 2 5 MGP3 0.73 6.49E−02 2 6 MGP3 0.92 3.74E−03 2 13MGP3 0.74 3.60E−02 5 12 MGP3 0.81 1.51E−02 5 15 Provided are thecorrelations (R) between the expression levels yield improving genes andtheir homologs in various tissues [Expression (Exp) sets] and thephenotypic performance [yield, biomass, growth rate and/or vigorcomponents (Correlation vector (Corr.))] under normal, low nitrogen anddrought conditions across barley varieties. P = p value.

TABLE 28 Correlation between the expression level of selected genes ofsome embodiments of the invention in various tissues and the phenotypicperformance of maintenance of performance under drought conditionsacross Barley accessions Gene Exp. Corr. Gene Exp. Corr. Name R P valueset Set ID Name R P value set Set ID LGP20 0.78 6.53E−02 1 3 LGP20 0.753.11E−02 5 6 LGP20 0.75 3.38E−02 5 5 LGP20 0.78 1.23E−02 4 2 LGP21 0.911.06E−02 1 16 LGP21 0.72 6.86E−02 2 20 LGP21 0.79 1.21E−02 4 2 LGP220.82 7.19E−03 4 2 LGP83 0.71 3.19E−02 6 16 LGP83 0.83 8.43E−03 2 16LGP83 0.76 2.94E−02 5 18 MGP3 0.92 1.86E−02 1 6 MGP3 0.91 1.10E−02 1 17MGP3 0.89 1.58E−02 1 15 MGP3 0.79 6.40E−02 1 20 MGP3 0.90 1.58E−02 1 5MGP3 0.96 2.23E−03 1 9 MGP3 0.76 7.71E−02 1 18 MGP3 0.80 5.49E−02 1 7MGP3 0.71 5.03E−02 3 16 MGP3 0.77 2.60E−02 3 17 MGP3 0.84 1.90E−02 3 8MGP3 0.73 2.60E−02 6 18 MGP3 0.71 3.16E−02 6 3 MGP3 0.75 5.16E−02 2 10MGP3 0.89 1.80E−02 5 8 MGP3 0.75 5.24E−02 5 11 Correlations (R) betweenthe genes expression levels in various tissues and the phenotypicperformance. “Corr. ID”—correlation set ID according to the correlatedparameters Table above. “Exp. Set”—Expression set. “R” = Pearsoncorrelation coefficient; “P” = p value.

Example 5 Production of Barley Transcriptome and High ThroughputCorrelation Analysis Using 60K Barley Oligonucleotide Micro-Array

In order to produce a high throughput correlation analysis, the presentinventors utilized a Barley oligonucleotide micro-array, produced byAgilent Technologies [chem. (dot) agilent (dot) com/Scripts/PDS (dot)asp?1Page=50879]. The array oligonucleotide represents about 33,777Barley genes and transcripts. In order to define correlations betweenthe levels of RNA expression and yield or vigor related parameters,various plant characteristics of 55 different Barley accessions wereanalyzed. Same accessions were subjected to RNA expression analysis. Thecorrelation between the RNA levels and the characterized parameters wasanalyzed using Pearson correlation test [davidmlane (dot)com/hyperstat/A34739 (dot) html].

Experimental Procedures

Four tissues at different developmental stages [leaf, flag leaf, spikeand peduncle], representing different plant characteristics, weresampled and RNA was extracted as described hereinabove under “GENERALEXPERIMENTAL AND BIOINFORMATICS METHODS”.

For convenience, each micro-array expression information tissue type hasreceived a Set ID as summarized in Table 29 below.

TABLE 29 Barley transcriptome expression sets Expression Set Set ID Flagleaf at booting stage under normal conditions 1 Spike at grain fillingstage under normal conditions 2 Spike at booting stage under normalconditions 3 stem at booting stage under normal conditions 4 Table 29:Provided are the identification (ID) letters of each of the Barleyexpression sets.

Barley yield components and vigor related parameters assessment—55Barley accessions in 5 repetitive blocks (named A, B, C, D and E), eachcontaining 48 plants per plot were grown in field. Plants werephenotyped on a daily basis. Harvest was conducted while 50% of thespikes were dry to avoid spontaneous release of the seeds. All materialwas oven dried and the seeds were threshed manually from the spikesprior to measurement of the seed characteristics (weight and size) usingscanning and image analysis. The image analysis system included apersonal desktop computer (Intel P4 3.0 GHz processor) and a publicdomain program—ImageJ 1.37 (Java based image processing program, whichwas developed at the U.S. National Institutes of Health and freelyavailable on the internet [rsbweb (dot) nih (dot) gov/]. Next, analyzeddata was saved to text files and processed using the JMP statisticalanalysis software (SAS institute).

At the end of the experiment (50% of the spikes were dry) all spikesfrom plots within blocks A-E were collected, and the followingmeasurements were performed:

% reproductive tiller percentage—The percentage of reproductive tillersat flowering calculated using Formula XXVI above.

1000 grain weight (gr)—At the end of the experiment all grains from allplots were collected and weighted and the weight of 1000 werecalculated.

Avr. (average) seedling dry weight (gr)—Weight of seedling afterdrying/number of plants.

Avr. shoot dry weight (gr)—Weight of Shoot at flowering stage afterdrying/number of plants.

Avr. spike weight (g)—Calculate spikes dry weight after drying at 70° C.in oven for 48 hours, at harvest/num of spikes.

Spike weight—The biomass and spikes weight of each plot was separated,measured and divided by the number of plants.

Dry weight—total weight of the vegetative portion above ground(excluding roots) after drying at 70° C. in oven for 48 hours at twotime points at the Vegetative growth (30 days after sowing) and atharvest.

Vegetative dry weight (g)—Total weight of the vegetative portion aboveground (excluding roots) after drying at 70° C. in oven for 48 hours.The biomass weight of each plot was measured and divided by the numberof plants.

Field spike length (cm)—Measure spike length without the Awns atharvest.

Grain Area (cm²)—A sample of ˜200 grains was weighted, photographed andimages were processed using the below described image processing system.The grain area was measured from those images and was divided by thenumber of grains.

Grain Length and Grain width (cm)—A sample of ˜200 grains was weighted,photographed and images were processed using the below described imageprocessing system. The sum of grain lengths and width (longest axis) wasmeasured from those images and was divided by the number of grains.

Grain Perimeter (cm)—A sample of ˜200 grains was weighted, photographedand images were processed using the below described image processingsystem. The sum of grain perimeter was measured from those images andwas divided by the number of grains.

Grains per spike—The total number of grains from 5 spikes that weremanually threshed was counted. The average grain per spike wascalculated by dividing the total grain number by the number of spikes.

Grain yield per plant (gr)—The total grains from 5 spikes that weremanually threshed was weighted. The grain yield was calculated bydividing the total weight by the plants number.

Grain yield per spike (gr)—The total grains from 5 spikes that weremanually threshed was weighted. The grain yield was calculated bydividing the total weight by the spike number.

Growth habit scoring—At growth stage 10 (booting), each of the plantswas scored for its growth habit nature. The scale that was used was “1”for prostate nature till “9” for erect.

Harvest Index (for barley)—The harvest index was calculated usingFormula XVIII above.

Number of days to anthesis—Calculated as the number of days from sowingtill 50% of the plot reach anthesis.

Number of days to maturity—Calculated as the number of days from sowingtill 50% of the plot reach maturity.

Plant height—At harvest stage (50% of spikes were dry), each of theplants was measured for its height using measuring tape. Height wasmeasured from ground level to top of the longest spike excluding awns.

Reproductive period—Calculated number of days from booting to maturity.

Reproductive tillers number—Number of Reproductive tillers with flagleaf at flowering.

Relative Growth Rate (RGR) of vegetative dry weight was performed usingFormula VII above.

Spike area (cm²)—At the end of the growing period 5 ‘spikes’ were,photographed and images were processed using the below described imageprocessing system. The ‘spike’ area was measured from those images andwas divided by the number of ‘spikes’.

Spike length and width analysis—At the end of the experiment the lengthand width of five chosen spikes per plant were measured using measuringtape excluding the awns.

Spike max width—Measured by imaging the max width of 10-15 spikesrandomly distributed within a pre-defined 0.5 m² of a plot. Measurementswere carried out at the middle of the spike.

Spikes Index—The Spikes index was calculated using Formula XXVII above.

Spike number analysis—The spikes per plant were counted at harvest.

No. of tillering—tillers were counted per plant at heading stage (meanper plot).

Total dry mater per plant—Calculated as Vegetative portion above groundplus all the spikes dry weight per plant.

TABLE 30 Barley correlated parameters (vectors) Correlated parameterwith Correlation ID % reproductive tiller percentage (%) 1 1000 grainweight (gr) 2 Avr spike dry weight per plant (H) (g) 3 Avr vegetativedry weight per plant (H) (g) 4 Avr shoot dry weight (F) (gr) 5 Avr spikeweight (H) (g) 6 Grain Perimeter (cm) 7 Grain Area (cm²) 8 Grain Length(cm) 9 Grain width (cm) 10 Grains per spike (number) 11 Grain yield perplant (gr) 12 Grain yield per spike (gr) 13 Growth habit (scores 1-9) 14Harvest Index (value) 15 Number days to anthesis (days) 16 Number daysto maturity (days) 17 Plant height (cm) 18 RGR 19 Reproductive period(days) 20 Reproductive tillers number (F) (number) 21 Spike area (cm²)22 Spike length (cm) 23 Spike width (cm) 24 Spike max width (cm) 25Spike index (cm) 26 Spikes per plant (numbers) 27 Tillering (Heading)(number) 28 Total dry matter per plant (kg) 29 Avr seedling dry weight(gr) 30 Field spike length (cm) 31 Table 30. Provided are the Barleycorrelated parameters (vectors).

Experimental Results

55 different Barley accessions were grown and characterized for 31parameters as described above. Among the 55 lines and ecotypes, 27 areHordeum spontaneum and 19 are Hordeum vulgare. The average for each ofthe measured parameters was calculated using the JMP software and valuesare summarized in Tables 31 and 32 below. Subsequent correlationanalysis between the various transcriptome expression sets (Table 29)and the average parameters was conducted. Correlations were calculatedacross all 55 lines and ecotypes. For phenotypic data of all 55 linesand ecotypes see Tables 31-38. For correlation data of all 55 lines andecotypes see Table 46. For phenotypic data of Hordeum spontaneum linesand ecotypes see Tables 39-42. For correlation data of Hordeumspontaneum lines and ecotypes see Table 47. For phenotypic data ofHordeum vulgare lines and ecotypes see Tables 43-45. For correlationdata of Hordeum vulgare lines and ecotypes see Table 48.

TABLE 31 Measured parameters of correlation IDs in Barley accessions(1-7) Ecotype/Treatment Line-1 Line-2 Line-3 Line-4 Line-5 Line-6 Line-71 4.31 18.25 9.16 40.15 33.22 NA 7.86 2 50.11 49.98 31.77 52.43 47.2249.33 53.02 3 80.88 60.47 36.42 69.45 61.03 63.22 88.26 4 46.33 85.0382.74 127.37 79.51 82.95 68.92 5 11.34 52.57 48.28 126.89 60.56 NA 31.406 3.33 1.56 2.37 3.11 3.18 2.85 3.37 7 2.62 2.41 2.31 2.67 2.62 2.592.59 8 0.30 0.28 0.24 0.30 0.29 0.29 0.30 9 1.09 0.97 0.92 1.07 1.091.07 1.05 10 0.40 0.41 0.35 0.41 0.39 0.39 0.41 11 56.51 21.05 45.1644.35 47.12 43.51 55.88 12 64.98 37.47 NA 51.69 49.15 46.44 NA 13 2.911.02 1.37 2.33 2.23 2.14 2.85 14 4.20 1.00 1.40 2.60 2.60 1.00 2.60 150.51 0.25 NA 0.26 0.35 0.32 NA 16 90.80 124.40 122.00 NA 122.00 NA102.60 17 148.00 170.00 157.00 170.00 167.40 170.00 158.80 18 83.9779.87 99.04 122.46 108.03 87.00 97.03 19 2.45 3.96 3.91 4.75 4.12 NA3.24 20 57.20 45.60 35.00 NA 48.00 NA 56.20 21 1.00 9.20 5.00 19.2014.63 NA 2.80 22 9.90 7.82 9.68 11.07 10.17 9.98 9.94 23 9.49 10.26 7.887.97 8.42 8.12 7.61 24 1.23 0.87 1.44 1.68 1.47 1.51 1.57 25 1.41 1.051.59 1.79 1.60 1.61 1.70 26 0.64 0.42 0.30 0.35 0.44 0.43 0.56 27 45.2756.27 31.50 32.42 35.40 36.73 36.93 28 24.00 48.70 52.00 47.60 45.00 NA35.20 29 127.22 145.50 119.15 196.82 140.54 146.17 157.18 30 0.05 0.060.04 0.05 0.05 0.05 0.07 31 9.57 NA 7.66 7.93 8.13 NA 7.21 Table 31.Provided are the values of each of the parameters measured in Barleyaccessions (1-7) according to the correlation identifications (see Table30). “NA” = not available.

TABLE 32 Barley accessions (8-14), additional measured parametersEcotype/Treatment Line-8 Line-9 Line-10 Line-11 Line-12 Line-13 Line-141 16.67 5.64 5.29 18.34 4.03 8.83 4.82 2 61.33 49.97 51.70 56.46 53.9750.36 56.81 3 91.89 99.05 66.99 60.22 87.61 71.76 76.71 4 82.88 56.8064.14 54.23 73.23 49.50 47.63 5 44.57 9.71 38.18 46.74 42.32 11.62 9.336 4.13 3.47 3.15 1.88 3.35 3.60 3.24 7 2.78 2.66 2.63 2.28 2.54 2.372.71 8 0.33 0.29 0.30 0.28 0.30 0.27 0.32 9 1.15 1.09 1.08 0.88 1.030.96 1.12 10 0.42 0.39 0.39 0.45 0.42 0.41 0.41 11 58.33 56.03 59.0827.27 55.87 61.53 50.80 12 78.18 79.86 54.34 46.37 71.89 56.24 61.63 133.47 2.60 2.84 1.51 2.84 2.98 2.85 14 1.00 5.00 3.00 1.00 1.00 2.20 3.0015 0.45 0.51 0.41 0.40 0.45 0.48 0.50 16 111.60 86.80 106.20 117.80111.60 85.40 90.00 17 156.20 159.60 157.00 162.20 159.60 157.00 150.5018 104.01 70.78 98.11 57.88 94.52 73.20 78.65 19 3.82 2.30 3.60 3.833.63 2.43 2.26 20 44.60 72.80 50.80 44.40 46.00 71.60 61.50 21 6.30 1.202.10 10.00 2.60 1.63 1.00 22 9.89 9.58 11.19 8.76 10.49 10.83 11.23 236.39 7.73 8.45 10.55 7.60 7.87 9.42 24 1.83 1.50 1.57 0.96 1.63 1.631.43 25 1.93 1.59 1.71 1.17 1.75 1.72 1.58 26 0.51 0.64 0.51 0.53 0.550.61 0.62 27 32.10 48.53 29.80 50.80 32.40 26.80 42.42 28 38.50 21.5036.10 57.25 42.20 19.13 21.63 29 178.63 155.85 131.13 114.45 160.84121.26 124.34 30 0.05 0.06 0.05 0.06 0.06 0.06 0.05 31 5.65 7.94 8.5510.59 7.44 7.36 9.60 Table 32. Provided are the values of each of theparameters measured in Barley accessions (8-14) according to thecorrelation identifications (see Table 30).

TABLE 33 Barley accessions (15-21), additional measured parameters Line-Line- Line- Line- Line- Line- Line- Ecotype/Treatment 15 16 17 18 19 2021 1 29.49 5.01 3.74 11.42 5.13 4.07 6.62 2 57.98 51.44 58.07 53.4548.66 39.48 41.96 3 81.14 77.90 68.17 70.73 54.13 48.72 64.51 4 66.5177.50 81.58 67.92 81.05 66.73 91.79 5 47.56 30.93 NA 35.49 38.41 NA41.56 6 3.12 1.69 1.66 3.50 1.16 2.95 1.36 7 2.90 2.28 2.42 2.65 2.162.16 2.45 8 0.34 0.27 0.30 0.30 0.26 0.23 0.23 9 1.22 0.89 0.96 1.080.83 0.85 0.94 10 0.41 0.42 0.44 0.40 0.42 0.39 0.36 11 45.48 24.7721.15 59.72 17.46 63.19 19.87 12 64.82 56.43 49.68 54.97 40.33 NA NA 132.39 1.21 1.18 2.93 0.83 2.38 0.78 14 1.00 1.00 3.80 3.80 1.00 3.40 1.0015 0.44 0.36 0.33 0.40 0.29 NA NA 16 113.20 113.40 98.50 109.60 119.4098.80 119.40 17 158.00 170.00 170.00 155.20 170.00 156.20 170.00 1890.73 64.27 82.73 94.12 63.47 102.12 94.80 19 3.89 3.46 NA 3.60 3.64 NA3.74 20 44.80 56.60 71.50 45.60 50.60 57.40 50.60 21 17.00 3.00 1.003.80 4.20 1.00 4.63 22 7.89 9.15 8.57 11.30 7.04 8.37 7.28 23 6.68 12.0510.74 8.60 8.94 6.03 10.99 24 1.45 0.88 0.92 1.56 0.92 1.67 0.76 25 1.521.03 1.10 1.72 1.08 1.75 0.90 26 0.55 0.50 0.45 0.51 0.39 0.42 0.41 2739.73 71.33 65.40 33.27 82.47 32.87 73.13 28 59.80 62.50 31.20 34.0078.90 26.50 69.88 29 147.66 155.41 149.76 138.64 135.18 115.45 156.29 300.05 0.04 0.05 0.04 0.06 0.05 0.05 31 6.23 NA NA 8.57 NA 6.26 NA Table33. Provided are the values of each of the parameters measured in Barleyaccessions (15-21) according to the correlation identifications (seeTable 30).

TABLE 34 Barley accessions (22-28), additional measured parameters Line-Line- Line- Line- Line- Line- Line- Ecotype/Treatment 22 23 24 25 26 2728 1 3.51 7.34 31.12 NA NA 11.07 21.67 2 18.60 42.65 39.67 24.43 28.4228.40 23.52 3 33.60 33.22 52.10 33.28 47.69 52.78 52.54 4 50.17 45.2267.20 43.40 79.51 61.09 59.71 5 174.82 8.39 51.83 NA NA 38.46 38.79 60.90 3.09 1.22 0.91 0.92 1.08 0.95 7 2.65 2.19 2.44 2.90 2.62 2.66 2.688 0.25 0.25 0.25 0.27 0.25 0.25 0.24 9 1.11 0.88 0.96 1.20 1.07 1.081.11 10 0.31 0.39 0.37 0.32 0.32 0.33 0.31 11 16.30 60.49 17.54 12.0020.01 20.00 17.01 12 NA NA NA NA NA NA NA 13 0.31 2.43 0.67 0.31 0.560.56 0.38 14 1.00 3.00 1.00 1.00 1.00 1.00 1.00 15 NA NA NA NA NA NA NA16 95.60 90.00 111.00 83.60 122.00 111.40 109.20 17 133.00 161.40 145.80140.20 153.00 143.00 140.40 18 90.49 88.53 90.10 92.47 99.08 91.69 94.6719 5.01 2.12 3.97 NA NA 3.67 3.68 20 37.40 71.40 34.80 56.60 31.00 31.6031.20 21 1.88 1.00 15.50 NA NA 7.10 15.70 22 4.98 11.56 6.52 5.39 8.168.08 5.73 23 8.58 9.02 8.63 7.96 10.20 10.52 8.35 24 0.68 1.53 0.88 0.810.97 0.92 0.78 25 0.79 1.68 1.01 0.88 1.05 1.01 0.90 26 0.41 0.42 0.440.44 0.38 0.46 0.47 27 88.07 20.53 48.53 51.33 65.80 55.80 65.60 2855.25 14.00 48.50 NA NA 69.00 76.40 29 83.76 78.44 119.30 76.68 127.20113.88 112.25 30 0.03 0.06 0.05 0.05 0.04 0.05 0.05 31 9.74 9.06 8.698.90 10.13 10.61 9.60 Table 34. Provided are the values of each of theparameters measured in Barley accessions (22-28) according to thecorrelation identifications (see Table 30).

TABLE 35 Barley accessions (29-35), additional measured parameters Line-Line- Line- Line- Line- Line- Line- Ecotype/Treatment 29 30 31 32 33 3435 1 3.93 16.51 3.19 10.55 26.51 15.15 4.28 2 45.71 26.47 23.14 27.6429.37 27.74 42.12 3 83.98 47.05 48.92 47.26 48.82 46.56 89.21 4 45.3660.37 67.39 67.12 61.35 59.03 71.31 5 10.63 29.60 14.28 37.74 39.2334.46 41.16 6 2.99 0.85 0.85 0.89 1.10 1.09 2.93 7 2.77 2.66 2.57 2.933.16 2.99 2.97 8 0.30 0.25 0.24 0.29 0.33 0.29 0.30 9 1.13 1.09 1.061.23 1.33 1.27 1.16 10 0.39 0.32 0.32 0.33 0.34 0.32 0.39 11 56.85 18.1913.50 12.83 14.49 13.72 54.84 12 NA NA NA NA NA NA NA 13 2.63 0.46 0.310.37 0.43 0.39 2.14 14 2.20 1.00 1.00 1.00 1.00 1.00 1.00 15 NA NA NA NANA NA NA 16 89.20 104.00 89.20 97.80 113.60 109.20 110.40 17 151.60140.20 140.40 140.40 145.80 143.00 156.20 18 66.65 105.78 112.21 103.83105.74 107.45 100.65 19 2.37 3.42 2.67 3.64 3.65 3.51 3.74 20 62.4036.20 51.20 42.60 32.20 33.80 45.80 21 1.00 12.30 1.10 8.50 18.67 11.002.50 22 8.94 4.69 5.47 5.92 6.16 6.88 11.03 23 7.75 6.85 8.51 8.32 9.809.28 8.77 24 1.37 0.81 0.75 0.83 0.74 0.88 1.53 25 1.52 0.91 0.85 0.960.82 0.94 1.60 26 0.65 0.44 0.42 0.41 0.41 0.44 0.56 27 44.87 77.1385.00 67.53 50.87 55.67 38.60 28 26.50 76.60 35.30 75.30 68.50 66.8055.80 29 129.34 107.42 116.31 114.38 104.47 105.59 160.52 30 0.05 0.040.04 0.05 0.04 0.06 0.05 31 7.97 8.24 9.14 8.71 9.82 10.00 8.47 Table35. Provided are the values of each of the parameters measured in Barleyaccessions (29-35) according to the correlation identifications (seeTable 30).

TABLE 36 Barley accessions (36-42), additional measured parameters Line-Line- Line- Line- Line- Line- Line- Ecotype/Treatment 36 37 38 39 40 4142 1 9.46 4.75 NA 4.60 21.49 21.20 14.49 2 26.38 19.78 31.00 47.79 32.5736.89 24.24 3 43.46 27.36 44.56 69.91 44.21 50.54 44.04 4 48.56 31.4659.31 43.15 72.36 91.79 63.37 5 23.84 11.91 NA 8.31 55.42 55.88 31.34 60.74 1.15 1.32 3.51 1.45 1.40 0.93 7 3.17 2.74 2.69 2.93 2.38 2.67 3.058 0.30 0.26 0.26 0.32 0.23 0.28 0.30 9 1.30 1.11 1.10 1.21 0.95 1.091.28 10 0.31 0.32 0.33 0.39 0.33 0.36 0.33 11 11.25 16.11 21.71 58.2034.19 20.75 11.50 12 NA NA NA NA NA NA NA 13 0.24 0.32 0.66 2.82 0.940.75 0.31 14 1.00 1.00 1.00 3.80 1.00 1.40 1.00 15 NA NA NA NA NA NA NA16 108.40 91.60 115.60 84.20 118.00 116.80 111.00 17 140.40 133.00145.80 148.00 153.80 144.20 140.20 18 106.34 78.29 107.63 77.57 93.91126.08 107.15 19 3.17 2.50 NA 2.12 4.03 NA 3.44 20 32.00 41.40 30.2063.80 36.00 27.40 29.25 21 7.40 1.50 NA 0.81 14.80 15.50 10.70 22 5.177.72 8.37 7.41 7.83 8.38 5.09 23 7.81 11.96 11.32 7.52 8.33 10.12 8.2724 0.79 0.75 0.86 1.16 1.15 0.99 0.72 25 0.91 0.92 0.94 1.31 1.24 1.060.82 26 0.47 0.48 0.43 0.62 0.37 0.36 0.41 27 64.67 50.93 48.40 32.0043.40 45.80 73.53 28 69.30 32.20 NA 15.81 66.40 75.13 71.20 29 92.0258.82 110.88 113.06 116.57 149.88 107.41 30 0.06 0.03 0.04 0.06 0.05 NA0.06 31 8.36 12.49 11.03 8.21 7.97 10.44 8.66 Table 36. Provided are thevalues of each of the parameters measured in Barley accessions (36-42)according to the correlation identifications (see Table 30).

TABLE 37 Barley accessions (43-49), additional measured parameters Line-Line- Line- Line- Line- Line- Line- Ecotype/Treatment 43 44 45 46 47 4849 1 17.05 12.52 9.87 10.75 10.80 14.99 16.12 2 27.81 23.34 31.77 27.3625.70 24.92 26.31 3 50.12 40.37 55.92 33.55 31.74 50.70 44.59 4 69.4158.51 61.56 42.29 41.24 71.38 73.03 5 32.88 35.99 42.56 19.47 26.1639.22 49.89 6 0.96 0.82 1.34 1.16 1.18 0.94 1.05 7 2.77 2.94 3.18 3.062.75 2.62 2.99 8 0.26 0.29 0.33 0.30 0.26 0.24 0.29 9 1.14 1.25 1.321.25 1.13 1.06 1.25 10 0.33 0.32 0.35 0.34 0.32 0.32 0.33 11 17.55 10.6515.98 14.58 17.44 18.90 14.60 12 NA NA NA NA NA NA NA 13 0.47 0.25 0.530.43 0.45 0.47 0.40 14 1.00 1.00 1.00 1.00 1.00 1.00 1.00 15 NA NA NA NANA NA NA 16 111.00 111.00 111.00 99.20 105.80 111.00 117.20 17 146.00140.20 143.00 133.00 133.00 143.00 148.20 18 106.69 96.26 99.81 91.7580.80 105.57 101.87 19 3.52 3.60 3.75 2.94 3.29 3.68 3.84 20 35.00 29.2032.00 33.80 27.20 32.00 31.00 21 15.00 11.70 6.90 5.50 10.30 12.40 13.3322 5.03 4.88 8.33 7.43 6.71 6.61 7.10 23 8.45 7.95 10.21 11.52 10.179.09 9.79 24 0.65 0.72 0.96 0.76 0.77 0.94 0.85 25 0.76 0.82 1.04 0.910.92 0.97 0.95 26 0.42 0.41 0.48 0.44 0.46 0.42 0.38 27 79.33 61.6749.13 55.10 56.67 62.20 70.93 28 86.70 90.70 71.40 58.50 90.90 87.50108.50 29 119.53 98.88 117.49 75.84 72.98 122.08 117.62 30 0.04 0.030.05 0.05 0.04 0.07 0.05 31 9.91 8.51 10.18 11.82 10.58 9.42 10.04 Table37. Provided are the values of each of the parameters measured in Barleyaccessions (43-49) according to the correlation identifications (seeTable 30).

TABLE 38 Barley accessions (50-55), additional measured parameters Line-Line- Line- Line- Line- Line- Ecotype/Treatment 50 51 52 53 54 55 131.13 NA 15.51 6.88 7.07 6.72 2 30.08 24.82 26.46 21.49 43.66 47.91 336.91 26.20 57.49 47.76 43.70 68.61 4 50.75 52.91 73.30 65.81 56.28 NA 537.91 NA 38.72 29.92 14.62 67.47 6 1.01 1.01 0.84 0.75 3.71 2.78 7 3.063.24 2.90 2.65 2.24 2.56 8 0.31 0.32 0.26 0.25 0.25 0.28 9 1.26 1.361.17 1.10 0.88 1.05 10 0.35 0.33 0.32 0.31 0.40 0.38 11 13.58 13.0719.84 17.16 65.39 43.77 12 NA NA NA NA 34.58 53.97 13 0.40 0.32 0.500.38 2.64 2.06 14 1.00 1.00 1.00 1.00 5.00 1.80 15 NA NA NA NA 0.35 NA16 113.00 122.60 111.00 107.60 88.40 128.00 17 143.60 152.00 142.40140.40 157.00 170.00 18 95.35 80.26 105.02 98.42 93.79 90.30 19 NA NA3.66 3.41 2.18 4.23 20 30.60 29.40 31.40 32.80 68.60 42.00 21 20.20 NA18.30 6.60 2.50 3.10 22 6.86 8.62 7.16 5.75 10.74 10.04 23 9.38 11.7310.01 8.78 8.54 8.59 24 0.87 0.87 0.86 0.77 1.49 1.45 25 0.94 0.97 0.940.89 1.68 1.57 26 0.42 0.33 0.44 0.42 0.44 NA 27 39.27 45.00 74.58 74.5320.80 38.00 28 64.60 NA 113.50 95.60 15.60 43.20 29 87.66 79.11 130.79113.58 99.98 NA 30 NA 0.04 0.04 0.05 0.05 0.05 31 9.41 11.67 10.60 9.728.26 9.22 Table 38. Provided are the values of each of the parametersmeasured in Barley accessions (50-55) according to the correlationidentifications (see Table 30).

TABLE 39 Barley accessions, additional measured parametersEcotype/Treatment Line-21 Line-22 Line-24 Line-25 Line-26 Line-27Line-28 1 6.62 3.51 31.12 NA NA 11.07 21.67 2 41.96 18.60 39.67 24.4328.42 28.40 23.52 3 64.51 33.60 52.10 33.28 47.69 52.78 52.54 4 91.7950.17 67.20 43.40 79.51 61.09 59.71 5 41.56 174.82 51.83 NA NA 38.4638.79 6 1.36 0.90 1.22 0.91 0.92 1.08 0.95 7 2.45 2.65 2.44 2.90 2.622.66 2.68 8 0.23 0.25 0.25 0.27 0.25 0.25 0.24 9 0.94 1.11 0.96 1.201.07 1.08 1.11 10 0.36 0.31 0.37 0.32 0.32 0.33 0.31 11 19.87 16.3017.54 12.00 20.01 20.00 17.01 12 NA NA NA NA NA NA NA 13 0.78 0.31 0.670.31 0.56 0.56 0.38 14 1.00 1.00 1.00 1.00 1.00 1.00 1.00 15 NA NA NA NANA NA NA 16 119.40 95.60 111.00 83.60 122.00 111.40 109.20 17 170.00133.00 145.80 140.20 153.00 143.00 140.40 18 94.80 90.49 90.10 92.4799.08 91.69 94.67 19 3.74 5.01 3.97 NA NA 3.67 3.68 20 50.60 37.40 34.8056.60 31.00 31.60 31.20 21 4.63 1.88 15.50 NA NA 7.10 15.70 22 7.28 4.986.52 5.39 8.16 8.08 5.73 23 10.99 8.58 8.63 7.96 10.20 10.52 8.35 240.76 0.68 0.88 0.81 0.97 0.92 0.78 25 0.90 0.79 1.01 0.88 1.05 1.01 0.9026 0.41 0.41 0.44 0.44 0.38 0.46 0.47 27 73.13 88.07 48.53 51.33 65.8055.80 65.60 28 69.88 55.25 48.50 NA NA 69.00 76.40 29 156.29 83.76119.30 76.68 127.20 113.88 112.25 30 0.05 0.03 0.05 0.05 0.04 0.05 0.0531 NA 9.74 8.69 8.90 10.13 10.61 9.60 Table 39. Provided are the valuesof each of the parameters measured in Barley Hordeum spontaneumaccessions (21-22, 24-28) according to the correlation identifications(see Table 30).

TABLE 40 Barley accessions, additional measured parameters Line- Line-Line- Line- Line- Ecotype/Treatment Line30 Line-31 32 33 34 36 37 116.51 3.19 10.55 26.51 15.15 9.46 4.75 2 26.47 23.14 27.64 29.37 27.7426.38 19.78 3 47.05 48.92 47.26 48.82 46.56 43.46 27.36 4 60.37 67.3967.12 61.35 59.03 48.56 31.46 5 29.60 14.28 37.74 39.23 34.46 23.8411.91 6 0.85 0.85 0.89 1.10 1.09 0.74 1.15 7 2.66 2.57 2.93 3.16 2.993.17 2.74 8 0.25 0.24 0.29 0.33 0.29 0.30 0.26 9 1.09 1.06 1.23 1.331.27 1.30 1.11 10 0.32 0.32 0.33 0.34 0.32 0.31 0.32 11 18.19 13.5012.83 14.49 13.72 11.25 16.11 12 NA NA NA NA NA NA NA 13 0.46 0.31 0.370.43 0.39 0.24 0.32 14 1.00 1.00 1.00 1.00 1.00 1.00 1.00 15 NA NA NA NANA NA NA 16 104.00 89.20 97.80 113.60 109.20 108.40 91.60 17 140.20140.40 140.40 145.80 143.00 140.40 133.00 18 105.78 112.21 103.83 105.74107.45 106.34 78.29 19 3.42 2.67 3.64 3.65 3.51 3.17 2.50 20 36.20 51.2042.60 32.20 33.80 32.00 41.40 21 12.30 1.10 8.50 18.67 11.00 7.40 1.5022 4.69 5.47 5.92 6.16 6.88 5.17 7.72 23 6.85 8.51 8.32 9.80 9.28 7.8111.96 24 0.81 0.75 0.83 0.74 0.88 0.79 0.75 25 0.91 0.85 0.96 0.82 0.940.91 0.92 26 0.44 0.42 0.41 0.41 0.44 0.47 0.48 27 77.13 85.00 67.5350.87 55.67 64.67 50.93 28 76.60 35.30 75.30 68.50 66.80 69.30 32.20 29107.42 116.31 114.38 104.47 105.59 92.02 58.82 30 0.04 0.04 0.05 0.040.06 0.06 0.03 31 8.24 9.14 8.71 9.82 10.00 8.36 12.49 Table 40.Provided are the values of each of the parameters measured in BarleyHordeum spontaneum accessions (30-34, 36-37) according to thecorrelation identifications (see Table 30).

TABLE 41 Barley accessions, additional measured parametersEcotype/Treatment Line-38 Line-41 Line-42 Line-43 Line-44 Line-45Line-46 1 NA 21.20 14.49 17.05 12.52 9.87 10.75 2 31.00 36.89 24.2427.81 23.34 31.77 27.36 3 44.56 50.54 44.04 50.12 40.37 55.92 33.55 459.31 91.79 63.37 69.41 58.51 61.56 42.29 5 NA 55.88 31.34 32.88 35.9942.56 19.47 6 1.32 1.40 0.93 0.96 0.82 1.34 1.16 7 2.69 2.67 3.05 2.772.94 3.18 3.06 8 0.26 0.28 0.30 0.26 0.29 0.33 0.30 9 1.10 1.09 1.281.14 1.25 1.32 1.25 10 0.33 0.36 0.33 0.33 0.32 0.35 0.34 11 21.71 20.7511.50 17.55 10.65 15.98 14.58 12 NA NA NA NA NA NA NA 13 0.66 0.75 0.310.47 0.25 0.53 0.43 14 1.00 1.40 1.00 1.00 1.00 1.00 1.00 15 NA NA NA NANA NA NA 16 115.60 116.80 111.00 111.00 111.00 111.00 99.20 17 145.80144.20 140.20 146.00 140.20 143.00 133.00 18 107.63 126.08 107.15 106.6996.26 99.81 91.75 19 NA NA 3.44 3.52 3.60 3.75 2.94 20 30.20 27.40 29.2535.00 29.20 32.00 33.80 21 NA 15.50 10.70 15.00 11.70 6.90 5.50 22 8.378.38 5.09 5.03 4.88 8.33 7.43 23 11.32 10.12 8.27 8.45 7.95 10.21 11.5224 0.86 0.99 0.72 0.65 0.72 0.96 0.76 25 0.94 1.06 0.82 0.76 0.82 1.040.91 26 0.43 0.36 0.41 0.42 0.41 0.48 0.44 27 48.40 45.80 73.53 79.3361.67 49.13 55.10 28 NA 75.13 71.20 86.70 90.70 71.40 58.50 29 110.88149.88 107.41 119.53 98.88 117.49 75.84 30 0.04 NA 0.06 0.04 0.03 0.050.05 31 11.03 10.44 8.66 9.91 8.51 10.18 11.82 Table 41. Provided arethe values of each of the parameters measured in Barley Hordeumspontaneum accessions (38, 41-46) according to the correlationidentifications (see Table 30).

TABLE 42 Barley accessions, additional measured parametersEcotype/Treatment Line-47 Line-48 Line-49 Line-51 Line-52 Line-53 110.80 14.99 16.12 NA 15.51 6.88 2 25.70 24.92 26.31 24.82 26.46 21.49 331.74 50.70 44.59 26.20 57.49 47.76 4 41.24 71.38 73.03 52.91 73.3065.81 5 26.16 39.22 49.89 NA 38.72 29.92 6 1.18 0.94 1.05 1.01 0.84 0.757 2.75 2.62 2.99 3.24 2.90 2.65 8 0.26 0.24 0.29 0.32 0.26 0.25 9 1.131.06 1.25 1.36 1.17 1.10 10 0.32 0.32 0.33 0.33 0.32 0.31 11 17.44 18.9014.60 13.07 19.84 17.16 12 NA NA NA NA NA NA 13 0.45 0.47 0.40 0.32 0.500.38 14 1.00 1.00 1.00 1.00 1.00 1.00 15 NA NA NA NA NA NA 16 105.80111.00 117.20 122.60 111.00 107.60 17 133.00 143.00 148.20 152.00 142.40140.40 18 80.80 105.57 101.87 80.26 105.02 98.42 19 3.29 3.68 3.84 NA3.66 3.41 20 27.20 32.00 31.00 29.40 31.40 32.80 21 10.30 12.40 13.33 NA18.30 6.60 22 6.71 6.61 7.10 8.62 7.16 5.75 23 10.17 9.09 9.79 11.7310.01 8.78 24 0.77 0.94 0.85 0.87 0.86 0.77 25 0.92 0.97 0.95 0.97 0.940.89 26 0.46 0.42 0.38 0.33 0.44 0.42 27 56.67 62.20 70.93 45.00 74.5874.53 28 90.90 87.50 108.50 NA 113.50 95.60 29 72.98 122.08 117.62 79.11130.79 113.58 30 0.04 0.07 0.05 0.04 0.04 0.05 31 10.58 9.42 10.04 11.6710.60 9.72 Table 42. Provided are the values of each of the parametersmeasured in Barley Hordeum spontaneum accessions (47-49, 51-53)according to the correlation identifications (see Table 30).

TABLE 43 Barley accessions, additional measured parametersEcotype/Treatment Line-1 Line-2 Line-4 Line-5 Line-6 Line-8 Line-9 14.31 18.25 40.15 33.22 NA 16.67 5.64 2 50.11 49.98 52.43 47.22 49.3361.33 49.97 3 80.88 60.47 69.45 61.03 63.22 91.89 99.05 4 46.33 85.03127.37 79.51 82.95 82.88 56.80 5 11.34 52.57 126.89 60.56 NA 44.57 9.716 3.33 1.56 3.11 3.18 2.85 4.13 3.47 7 2.62 2.41 2.67 2.62 2.59 2.782.66 8 0.30 0.28 0.30 0.29 0.29 0.33 0.29 9 1.09 0.97 1.07 1.09 1.071.15 1.09 10 0.40 0.41 0.41 0.39 0.39 0.42 0.39 11 56.51 21.05 44.3547.12 43.51 58.33 56.03 12 64.98 37.47 51.69 49.15 46.44 78.18 79.86 132.91 1.02 2.33 2.23 2.14 3.47 2.60 14 4.20 1.00 2.60 2.60 1.00 1.00 5.0015 0.51 0.25 0.26 0.35 0.32 0.45 0.51 16 90.80 124.40 NA 122.00 NA111.60 86.80 17 148.00 170.00 170.00 167.40 170.00 156.20 159.60 1883.97 79.87 122.46 108.03 87.00 104.01 70.78 19 2.45 3.96 4.75 4.12 NA3.82 2.30 20 57.20 45.60 NA 48.00 NA 44.60 72.80 21 1.00 9.20 19.2014.63 NA 6.30 1.20 22 9.90 7.82 11.07 10.17 9.98 9.89 9.58 23 9.49 10.267.97 8.42 8.12 6.39 7.73 24 1.23 0.87 1.68 1.47 1.51 1.83 1.50 25 1.411.05 1.79 1.60 1.61 1.93 1.59 26 0.64 0.42 0.35 0.44 0.43 0.51 0.64 2745.27 56.27 32.42 35.40 36.73 32.10 48.53 28 24.00 48.70 47.60 45.00 NA38.50 21.50 29 127.22 145.50 196.82 140.54 146.17 178.63 155.85 30 0.050.06 0.05 0.05 0.05 0.05 0.06 31 9.57 NA 7.93 8.13 NA 5.65 7.94 Table43. Provided are the values of each of the parameters measured in BarleyHordeum vulgare accessions (1-2, 4-6, 8-9) according to the correlationidentifications (see Table 30).

TABLE 44 Barley accessions, additional measured parametersEcotype/Treatment Line-10 Line-11 Line-12 Line-13 Line-14 Line-15Line-16 1 5.29 18.34 4.03 8.83 4.82 29.49 5.01 2 51.70 56.46 53.97 50.3656.81 57.98 51.44 3 66.99 60.22 87.61 71.76 76.71 81.14 77.90 4 64.1454.23 73.23 49.50 47.63 66.51 77.50 5 38.18 46.74 42.32 11.62 9.33 47.5630.93 6 3.15 1.88 3.35 3.60 3.24 3.12 1.69 7 2.63 2.28 2.54 2.37 2.712.90 2.28 8 0.30 0.28 0.30 0.27 0.32 0.34 0.27 9 1.08 0.88 1.03 0.961.12 1.22 0.89 10 0.39 0.45 0.42 0.41 0.41 0.41 0.42 11 59.08 27.2755.87 61.53 50.80 45.48 24.77 12 54.34 46.37 71.89 56.24 61.63 64.8256.43 13 2.84 1.51 2.84 2.98 2.85 2.39 1.21 14 3.00 1.00 1.00 2.20 3.001.00 1.00 15 0.41 0.40 0.45 0.48 0.50 0.44 0.36 16 106.20 117.80 111.6085.40 90.00 113.20 113.40 17 157.00 162.20 159.60 157.00 150.50 158.00170.00 18 98.11 57.88 94.52 73.20 78.65 90.73 64.27 19 3.60 3.83 3.632.43 2.26 3.89 3.46 20 50.80 44.40 46.00 71.60 61.50 44.80 56.60 21 2.1010.00 2.60 1.63 1.00 17.00 3.00 22 11.19 8.76 10.49 10.83 11.23 7.899.15 23 8.45 10.55 7.60 7.87 9.42 6.68 12.05 24 1.57 0.96 1.63 1.63 1.431.45 0.88 25 1.71 1.17 1.75 1.72 1.58 1.52 1.03 26 0.51 0.53 0.55 0.610.62 0.55 0.50 27 29.80 50.80 32.40 26.80 42.42 39.73 71.33 28 36.1057.25 42.20 19.13 21.63 59.80 62.50 29 131.13 114.45 160.84 121.26124.34 147.66 155.41 30 0.05 0.06 0.06 0.06 0.05 0.05 0.04 31 8.55 10.597.44 7.36 9.60 6.23 NA Table 44. Provided are the values of each of theparameters measured in Barley Hordeum vulgare accessions (10-16)according to the correlation identifications (see Table 30).

TABLE 45 Barley accessions, additional measured parametersEcotype/Treatment Line-17 Line-18 Line-19 Line-54 Line-55 1 3.74 11.425.13 7.07 6.72 2 58.07 53.45 48.66 43.66 47.91 3 68.17 70.73 54.13 43.7068.61 4 81.58 67.92 81.05 56.28 NA 5 NA 35.49 38.41 14.62 67.47 6 1.663.50 1.16 3.71 2.78 7 2.42 2.65 2.16 2.24 2.56 8 0.30 0.30 0.26 0.250.28 9 0.96 1.08 0.83 0.88 1.05 10 0.44 0.40 0.42 0.40 0.38 11 21.1559.72 17.46 65.39 43.77 12 49.68 54.97 40.33 34.58 53.97 13 1.18 2.930.83 2.64 2.06 14 3.80 3.80 1.00 5.00 1.80 15 0.33 0.40 0.29 0.35 NA 1698.50 109.60 119.40 88.40 128.00 17 170.00 155.20 170.00 157.00 170.0018 82.73 94.12 63.47 93.79 90.30 19 NA 3.60 3.64 2.18 4.23 20 71.5045.60 50.60 68.60 42.00 21 1.00 3.80 4.20 2.50 3.10 22 8.57 11.30 7.0410.74 10.04 23 10.74 8.60 8.94 8.54 8.59 24 0.92 1.56 0.92 1.49 1.45 251.10 1.72 1.08 1.68 1.57 26 0.45 0.51 0.39 0.44 NA 27 65.40 33.27 82.4720.80 38.00 28 31.20 34.00 78.90 15.60 43.20 29 149.76 138.64 135.1899.98 NA 30 0.05 0.04 0.06 0.05 0.05 31 NA 8.57 NA 8.26 9.22 Table 45.Provided are the values of each of the parameters measured in BarleyHordeum vulgare accessions (17-19, 54-55) according to the correlationidentifications (see Table 30).

TABLE 46 Correlation between the expression level of the selectedpolynucleotides of the invention and their homologues in specifictissues or developmental stages and the phenotypic performance acrossall 55 Barley accessions Gene Name R P value Exp. set Corr. Set ID LGP210.72 3.67E−09 4 26 Table 46. Provided are the correlations (R) andp-values (P) between the expression levels of selected genes of someembodiments of the invention in various tissues or developmental stages(Expression sets) and the phenotypic performance in various yield (seedyield, oil yield, oil content), biomass, growth rate and/or vigorcomponents [Correlation (Corr.) vector (Vec.) Expression (Exp.)] Corr.Vector = correlation vector specified in Table 30; Exp. Set = expressionset specified in Table 29.

TABLE 47 Correlation between the expression level of the selectedpolynucleotides of the invention and their homologues in specifictissues or developmental stages and the phenotypic performance across 27Barley Hordeum spontaneum accessions Gene Name R P value Exp. set Corr.Set ID MGP3 0.74 3.13E−04 2 21 Table 47. Provided are the correlations(R) and p-values (P) between the expression levels of selected genes ofsome embodiments of the invention in various tissues or developmentalstages (Expression sets) and the phenotypic performance in various yield(seed yield, oil yield, oil content), biomass, growth rate and/or vigorcomponents [Correlation (Corr.) vector (Vec.) Expression (Exp.)] Corr.Vector = correlation vector specified in Table 30; Exp. Set = expressionset specified in Table 29.

TABLE 48 Correlation between the expression level of the selectedpolynucleotides of the invention and their homologues in specifictissues or developmental stages and the phenotypic performance across 19Barley Hordeum vulgare accessions Gene Corr. Gene Corr. Name R P valueExp. set Set ID Name R P value Exp. set Set ID LGP21 0.74 6.16E−04 3 26LGP21 0.71 1.50E−03 4 26 LGP21 0.73 5.59E−04 2 8 Table 48. Provided arethe correlations (R) and p-values (P) between the expression levels ofselected genes of some embodiments of the invention in various tissuesor developmental stages (Expression sets) and the phenotypic performancein various yield (seed yield, oil yield, oil content), biomass, growthrate and/or vigor components [Correlation (Corr.) vector (Vec.)Expression (Exp.)] Con. Vector = correlation vector specified in Table30; Exp. Set = expression set specified in Table 29.

Example 6 Production of Arabidopsis Transcriptome and High ThroughputCorrelation Analysis of Yield, Biomass and/or Vigor Related ParametersUsing 44K Arabidopsis Full Genome Oligonucleotide Micro-Array

To produce a high throughput correlation analysis, the present inventorsutilized an Arabidopsis thaliana oligonucleotide micro-array, producedby Agilent Technologies [chem. (dot) agilent (dot) com/Scripts/PDS (dot)asp?1Page=50879]. The array oligonucleotide represents about 40,000 A.thaliana genes and transcripts designed based on data from the TIGR ATH1v.5 database and Arabidopsis MPSS (University of Delaware) databases. Todefine correlations between the levels of RNA expression and yield,biomass components or vigor related parameters, various plantcharacteristics of 15 different Arabidopsis ecotypes were analyzed.Among them, nine ecotypes encompassing the observed variance wereselected for RNA expression analysis. The correlation between the RNAlevels and the characterized parameters was analyzed using Pearsoncorrelation test [davidmlane (dot) com/hyperstat/A34739 (dot) html].

Experimental Procedures

Analyzed Arabidopsis tissues—Five tissues at different developmentalstages including root, leaf, flower at anthesis, seed at 5 days afterflowering (DAF) and seed at 12 DAF, representing different plantcharacteristics, were sampled and RNA was extracted as described asdescribed hereinabove under “GENERAL EXPERIMENTAL AND BIOINFORMATICSMETHODS”. For convenience, each micro-array expression informationtissue type has received a Set ID as summarized in Table 49 below.

TABLE 49 Tissues used for Arabidopsis transcriptome expression setsExpression Set Set ID Leaf 1 Root 2 Seed 5 DAF 3 Flower 4 Seed 12DAF 5Table 49: Provided are the identification (ID) digits of each of theArabidopsis expression sets (1-5). DAF = days after flowering.

Yield components and vigor related parameters assessment—Eight out ofthe nine Arabidopsis ecotypes were used in each of 5 repetitive blocks(named A, B, C, D and E), each containing 20 plants per plot. The plantswere grown in a greenhouse at controlled conditions in 22° C., and theN:P:K fertilizer (20:20:20; weight ratios) [nitrogen (N), phosphorus (P)and potassium (K)] was added. During this time data was collected,documented and analyzed. Additional data was collected through theseedling stage of plants grown in a tissue culture in vertical growntransparent agar plates. Most of chosen parameters were analyzed bydigital imaging.

Digital imaging in Tissue culture—A laboratory image acquisition systemwas used for capturing images of plantlets sawn in square agar plates.The image acquisition system consists of a digital reflex camera (CanonEOS 300D) attached to a 55 mm focal length lens (Canon EF-S series),mounted on a reproduction device (Kaiser RS), which included 4 lightunits (4×150 Watts light bulb) and located in a darkroom.

Digital imaging in Greenhouse—The image capturing process was repeatedevery 3-4 days starting at day 7 till day 30. The same camera attachedto a 24 mm focal length lens (Canon EF series), placed in a custom madeiron mount, was used for capturing images of larger plants sawn in whitetubs in an environmental controlled greenhouse. The white tubs weresquare shape with measurements of 36×26.2 cm and 7.5 cm deep. During thecapture process, the tubs were placed beneath the iron mount, whileavoiding direct sun light and casting of shadows. This process wasrepeated every 3-4 days for up to 30 days.

An image analysis system was used, which consists of a personal desktopcomputer (Intel P4 3.0 GHz processor) and a public domain program—ImageJ1.37, Java based image processing program, which was developed at theU.S National Institutes of Health and is freely available on theinternet at rsbweb (dot) nih (dot) gov/. Images were captured inresolution of 6 Mega Pixels (3072×2048 pixels) and stored in a lowcompression JPEG (Joint Photographic Experts Group standard) format.Next, analyzed data was saved to text files and processed using the JMPstatistical analysis software (SAS institute).

Leaf analysis—Using the digital analysis leaves data was calculated,including leaf number, area, perimeter, length and width. On day 30, 3-4representative plants were chosen from each plot of blocks A, B and C.The plants were dissected, each leaf was separated and was introducedbetween two glass trays, a photo of each plant was taken and the variousparameters (such as leaf total area, laminar length etc.) werecalculated from the images. The blade circularity was calculated aslaminar width divided by laminar length.

Root analysis—During 17 days, the different ecotypes were grown intransparent agar plates. The plates were photographed every 3 daysstarting at day 7 in the photography room and the roots development wasdocumented (see examples in FIGS. 3A-F). The growth rate of rootcoverage was calculated according to Formula XXVIII above.

Vegetative growth rate analysis—was calculated according to Formula VIIabove. The analysis was ended with the appearance of overlapping plants.

For comparison between ecotypes the calculated rate was normalized usingplant developmental stage as represented by the number of true leaves.In cases where plants with 8 leaves had been sampled twice (for exampleat day 10 and day 13), only the largest sample was chosen and added tothe Anova comparison.

Seeds in siliques analysis—On day 70, 15-17 siliques were collected fromeach plot in blocks D and E. The chosen siliques were light brown colorbut still intact. The siliques were opened in the photography room andthe seeds were scatter on a glass tray, a high resolution digitalpicture was taken for each plot. Using the images the number of seedsper silique was determined.

Seeds average weight—At the end of the experiment all seeds from plotsof blocks A-C were collected. An average weight of 0.02 grams wasmeasured from each sample, the seeds were scattered on a glass tray anda picture was taken. Using the digital analysis, the number of seeds ineach sample was calculated.

Oil percentage in seeds—At the end of the experiment all seeds fromplots of blocks A-C were collected. Columbia seeds from 3 plots weremixed grounded and then mounted onto the extraction chamber. 210 ml ofn-Hexane (Cat No. 080951 Biolab Ltd.) were used as the solvent. Theextraction was performed for 30 hours at medium heat 50° C. Once theextraction has ended the n-Hexane was evaporated using the evaporator at35° C. and vacuum conditions. The process was repeated twice. Theinformation gained from the Soxhlet extractor (Soxhlet, F. Diegewichtsanalytische Bestimmung des Milchfettes, Polytechnisches J.(Dingler's) 1879, 232, 461) was used to create a calibration curve forthe Low Resonance NMR. The content of oil of all seed samples wasdetermined using the Low Resonance NMR (MARAN Ultra—Oxford Instrument)and its MultiQuant software package.

Silique length analysis—On day 50 from sowing, 30 siliques fromdifferent plants in each plot were sampled in block A. The chosensiliques were green-yellow in color and were collected from the bottomparts of a grown plant's stem. A digital photograph was taken todetermine silique's length.

Dry weight and seed yield—On day 80 from sowing, the plants from blocksA-C were harvested and left to dry at 30° C. in a drying chamber. Thevegetative portion above ground was separated from the seeds. The totalweight of the vegetative portion above ground and the seed weight ofeach plot were measured and divided by the number of plants.

Dry weight (vegetative biomass)=total weight of the vegetative portionabove ground (excluding roots) after drying at 30° C. in a dryingchamber; all the above ground biomass that is not yield.

Seed yield per plant=total seed weight per plant (gr).

Oil yield—The oil yield was calculated using Formula XXIX above.

Harvest Index (seed)—The harvest index was calculated using Formula XV(described above).

Experimental Results

Nine different Arabidopsis ecotypes were grown and characterized for 18parameters (named as vectors).

TABLE 50 Arabidopsis correlated parameters (vectors) Correlatedparameter with Correlation ID Blade circularity (cm) 1 Dry matter perplant (gr) 2 Harvest Index (value) 3 Lamina length (cm) 4 Lamina width(cm) 5 Leaf width/length (ratio) 6 Oil % per seed (percent) 7 Oil yieldper plant (mg) 8 Seeds per silique (number) 9 Silique length (cm) 10Total Leaf Area per plant (cm²) 11 Vegetative growth rate (cm²/day)Until leaves were in 12 overlap Fresh weight (gr) (at bolting stage) 13Relative root growth (cm/day) in early seedling stages 14 Root lengthday 13 (cm) 15 Root length day 7 (cm) 16 1000 Seed weight (gr) 17 Seedyield per plant (gr) 18 Table 50. Provided are the Arabidopsiscorrelated parameters (correlation ID Nos. 1-18). Abbreviations: Cm =centimeter(s); gr = gram(s); mg = milligram(s).

The characterized values are summarized in Table 51. Correlationanalysis is provided in Table 52 below.

TABLE 51 Measured parameters in Arabidopsis ecotypes Ecotype/TreatmentLine-1 Line-2 Line-3 Line-4 Line-5 Line- 6 Line-7 Line-8 Line-9 1 0.510.48 0.45 0.37 0.50 0.38 0.39 0.49 0.41 2 0.64 1.27 1.05 1.28 1.69 1.340.81 1.21 1.35 3 0.53 0.35 0.56 0.33 0.37 0.32 0.45 0.51 0.41 4 2.773.54 3.27 3.78 3.69 4.60 3.88 3.72 4.15 5 1.38 1.70 1.46 1.37 1.83 1.651.51 1.82 1.67 6 0.35 0.29 0.32 0.26 0.36 0.27 0.30 0.34 0.31 7 34.4231.19 38.05 27.76 35.49 32.91 31.56 30.79 34.02 8 118.63 138.73 224.06116.26 218.27 142.11 114.15 190.06 187.62 9 45.44 53.47 58.47 35.2748.56 37.00 39.38 40.53 25.53 10 1.06 1.26 1.31 1.47 1.24 1.09 1.18 1.181.00 11 46.86 109.89 58.36 56.80 114.66 110.82 88.49 121.79 93.04 120.31 0.38 0.48 0.47 0.43 0.64 0.43 0.38 0.47 13 1.51 3.61 1.94 2.08 3.564.34 3.47 3.48 3.71 14 0.63 0.66 1.18 1.09 0.91 0.77 0.61 0.70 0.78 154.42 8.53 5.62 4.83 5.96 6.37 5.65 7.06 7.04 16 0.94 1.76 0.70 0.73 0.991.16 1.28 1.41 1.25 17 0.02 0.02 0.03 0.03 0.02 0.03 0.02 0.02 0.02 180.34 0.44 0.59 0.42 0.61 0.43 0.36 0.62 0.55 Table 51. Provided are thevalues of each of the parameters measured in Arabidopsis ecotypes.

TABLE 52 Correlation between the expression level of selected genes ofsome embodiments of the invention in various tissues and the phenotypicperformance under normal conditions across Arabidopsis accessions GeneExp. Corr. Gene Exp. Corr. Name R P value set Set ID Name R P value setSet ID LGP1 0.77 2.42E−02 5 17 LGP10 0.76 2.78E−02 4 4 LGP10 0.772.65E−02 4 13 LGP12 0.81 2.60E−02 3 3 LGP18 0.83 2.01E−02 3 3 LGP3 0.714.88E−02 4 4 LGP46 0.71 7.57E−02 3 10 LGP46 0.80 1.78E−02 4 15 LGP460.85 6.92E−03 1 17 LGP46 0.75 3.17E−02 1 2 LGP46 0.94 4.58E−04 1 5 LGP460.86 6.00E−03 1 11 LGP46 0.78 2.20E−02 1 10 LGP53 0.76 2.77E−02 2 17LGP53 0.75 3.06E−02 2 10 LGP53 0.76 4.63E−02 3 3 LGP53 0.80 1.83E−02 414 LGP59 0.73 4.00E−02 2 1 LGP59 0.79 2.06E−02 5 13 LGP59 0.91 1.99E−031 1 LGP6 0.81 2.73E−02 3 15 LGP8 0.81 1.45E−02 5 7 LYD691 0.76 4.75E−023 17 LYD693 0.72 6.85E−02 3 5 LYD693 0.80 1.60E−02 5 4 LYD693 0.938.21E−04 5 12 LYD693 0.76 2.74E−02 1 1 Table 52. Provided are thecorrelations (R) between the expression levels of yield improving genesand their homologues in tissues [leaf, flower, seed and root; Expressionsets (Exp)] and the phenotypic performance in various yield, biomass,growth rate and/or vigor components [Correlation vector (corr.)] undernormal conditions across Arabidopsis accessions. “Corr. ID”—correlationset ID according to the correlated parameters specified in Table 50.“Exp. Set”—Expression set specified in Table 50. “R” = Pearsoncorrelation coefficient; “P” = p value.

Example 7 Production of Arabidopsis Transcriptome and High ThroughputCorrelation Analysis of Normal and Nitrogen Limiting Conditions Using44K Arabidopsis Oligonucleotide Micro-Array

In order to produce a high throughput correlation analysis, the presentinventors utilized an Arabidopsis oligonucleotide micro-array, producedby Agilent Technologies [chem (dot) agilent (dot) com/Scripts/PDS (dot)asp?1Page=50879]. The array oligonucleotide represents about 44,000Arabidopsis genes and transcripts. To define correlations between thelevels of RNA expression with NUE, yield components or vigor relatedparameters various plant characteristics of 14 different Arabidopsisecotypes were analyzed. Among them, ten ecotypes encompassing theobserved variance were selected for RNA expression analysis. Thecorrelation between the RNA levels and the characterized parameters wasanalyzed using Pearson correlation test [davidmlane (dot)com/hyperstat/A34739 (dot) html].

Experimental Procedures

Two tissues of plants [leaves and stems] growing at two differentnitrogen fertilization levels (1.5 mM Nitrogen or 6 mM Nitrogen) weresampled and RNA was extracted as described hereinabove under “GENERALEXPERIMENTAL AND BIOINFORMATICS METHODS”. For convenience, eachmicro-array expression information tissue type has received a Set ID assummarized in Table 53 below.

TABLE 53 Tissues used for Arabidopsis transcriptome expression setsExpression Set Set ID Leaves at 6 mM Nitrogen fertilization 1 Leaves at1.5 mM Nitrogen fertilization 2 Stems at 1.5 mM Nitrogen fertilization 3Stems at 6 mM Nitrogen fertilization 4 Table 53: Provided are theidentification (ID) digits of each of the Arabidopsis expression sets.

Assessment of Arabidopsis yield components and vigor related parametersunder different nitrogen fertilization levels—10 Arabidopsis accessionsin 2 repetitive plots each containing 8 plants per plot were grown atgreenhouse. The growing protocol used was as follows: surface sterilizedseeds were sown in Eppendorf tubes containing 0.5× Murashige-Skoog basalsalt medium and grown at 23° C. under 12-hour light and 12-hour darkdaily cycles for 10 days. Then, seedlings of similar size were carefullytransferred to pots filled with a mix of perlite and peat in a 1:1ratio. Constant nitrogen limiting conditions were achieved by irrigatingthe plants with a solution containing 1.5 mM inorganic nitrogen in theform of KNO₃, supplemented with 2 mM CaCl₂, 1.25 mM KH₂PO₄, 1.50 mMMgSO₄, 5 mM KCl, 0.01 mM H₃BO₃ and microelements, while normalirrigation conditions (Normal Nitrogen conditions) was achieved byapplying a solution of 6 mM inorganic nitrogen also in the form of KNO₃,supplemented with 2 mM CaCl₂, 1.25 mM KH₂PO₄, 1.50 mM MgSO₄, 0.01 mMH₃BO₃ and microelements. To follow plant growth, trays were photographedthe day nitrogen limiting conditions were initiated and subsequentlyevery 3 days for about 15 additional days. Rosette plant area was thendetermined from the digital pictures. ImageJ software was used forquantifying the plant size from the digital pictures [rsb (dot) info(dot) nih (dot) gov/ij/] utilizing proprietary scripts designed toanalyze the size of rosette area from individual plants as a function oftime. The image analysis system included a personal desktop computer(Intel P4 3.0 GHz processor) and a public domain program—ImageJ 1.37(Java based image processing program, which was developed at the U.S.National Institutes of Health and freely available on the internet[rsbweb (dot) nih (dot) gov/]. Next, analyzed data was saved to textfiles and processed using the JMP statistical analysis software (SASinstitute).

Data parameters collected are summarized in Table 54, hereinbelow.

TABLE 54 Arabidopsis correlated parameters (vectors) Correlatedparameter with Correlation ID N 1.5 mM; 1000 Seeds weight [gr.] 1 N 1.5mM; % Biomass reduction compared to N 6 mM 2 N 1.5 mM; DW/N level[gr/SPAD unit] 3 N 1.5 mM; Dry Weight [gr./plant] 4 N 1.5 mM; HarvestIndex (ratio) 5 N 1.5 mM; Leaf Blade Area at day 10 [cm²] 6 N 1.5 mM;Leaf Number at day 10 (number) 7 N 1.5 mM; RGR of Rosette Area at day 3[cm²/day] 8 N 1.5 mM; Rosette Area at day 10 [cm²] 9 N 1.5 mM; RosetteArea at day 8 [cm²] 10 N 1.5 mM; N level/DW [SPAD unit/gr.] 11 N 1.5 mM;Seed Yield [gr./plant] 12 N 1.5 mM; % Seed yield reduction compared to N6 mM 13 N 1.5 mM; N level/FW [SPAD unit/gr.] 14 N 1.5 mM; seed yield/Nlevel [gr/SPAD unit] 15 N 1.5 mM; seed yield/leaf blade [gr./cm²] 16 N1.5 mM; seed yield/rosette area at day 10 [gr./cm²] 17 N 1.5 mM; t50Flowering [day] 18 N 6 mM; DW/N level [gr./SPAD unit] 19 N 6 mM; Nlevel/FW 20 N 6 mM; 1000 Seeds weight [gr.] 21 N 6 mM; Dry Weight[gr./plant] 22 N 6 mM; Harvest Index (ratio) 23 N 6 mM; Leaf Blade Areaat day 10 (cm²) 24 N 6 mM; Leaf Number at day 10 (number) 25 N 6 mM; RGRof Rosette Area at day 3 [cm²/gr.] 26 N 6 mM; Rosette Area at day 10[cm²] 27 N 6 mM; Rosette Area at day 8 [cm²] 28 N 6 mM; Seed Yield[gr./plant] 29 N 6 mM; Seed yield/N unit [gr./SPAD unit] 30 N 6 mM; seedyield/rosette area day at day 10 [gr./cm²] 31 N 6 mM; seed yield/leafblade [gr./cm²] 32 N 6 mM; N level/DW (SPAD unit/gr. plant) 33 N 6 mM;t50 Flowering [day] 34 Table 54. Provided are the Arabidopsis correlatedparameters (vectors). “N” = Nitrogen at the noted concentrations; “gr.”= grams; “SPAD” = chlorophyll levels; “t50” = time where 50% of plantsflowered; “gr./SPAD unit” = plant biomass expressed in grams per unit ofnitrogen in plant measured by SPAD. “DW” = Plant Dry Weight; “FW” =Plant Fresh weight; “N level/DW” = plant Nitrogen level measured in SPADunit per plant biomass [gr.]; “DW/N level” = plant biomass per plant[gr.]/SPAD unit; Rosette Area (measured using digital analysis); PlotCoverage at the indicated day [%] (calculated by the dividing the totalplant area with the total plot area); Leaf Blade Area at the indicatedday [cm²] (measured using digital analysis); RGR (relative growth rate)of Rosette Area at the indicated day [cm²/day]; t50 Flowering [day[ (theday in which 50% of plant flower); seed yield/rosette area at day 10[gr/cm²] (calculated); seed yield/leaf blade [gr/cm²] (calculated); seedyield/N level [gr/SPAD unit] (calculated).

Assessment of NUE, yield components and vigor-related parameters—TenArabidopsis ecotypes were grown in trays, each containing 8 plants perplot, in a greenhouse with controlled temperature conditions for about12 weeks. Plants were irrigated with different nitrogen concentration asdescribed above depending on the treatment applied. During this time,data was collected documented and analyzed. Most of chosen parameterswere analyzed by digital imaging.

Digital Imaging—Greenhouse Assay

An image acquisition system, which consists of a digital reflex camera(Canon EOS 400D) attached with a 55 mm focal length lens (Canon EF-Sseries) placed in a custom made Aluminum mount, was used for capturingimages of plants planted in containers within an environmentalcontrolled greenhouse. The image capturing process was repeated every2-3 days starting at day 9-12 till day 16-19 (respectively) fromtransplanting.

An image analysis system was used, which consists of a personal desktopcomputer (Intel P4 3.0 GHz processor) and a public domain program—ImageJ1.37, Java based image processing program, which was developed at theU.S National Institutes of Health and is freely available on theinternet at rsbweb (dot) nih (dot) gov/. Images were captured inresolution of 6 Mega Pixels (3072×2048 pixels) and stored in a lowcompression JPEG (Joint Photographic Experts Group standard) format.Next, analyzed data was saved to text files and processed using the JMPstatistical analysis software (SAS institute).

Leaf analysis—Using the digital analysis leaves data was calculated,including leaf number, leaf blade area, plot coverage, Rosette diameterand Rosette area.

Relative growth rate area: The relative growth rate area of the rosetteand the leaves was calculated according to Formulas IX and XIII,respectively, above.

Seed yield and 1000 seeds weight—At the end of the experiment all seedsfrom all plots were collected and weighed in order to measure seed yieldper plant in terms of total seed weight per plant (gr.). For thecalculation of 1000 seed weight, an average weight of 0.02 grams wasmeasured from each sample, the seeds were scattered on a glass tray anda picture was taken. Using the digital analysis, the number of seeds ineach sample was calculated.

Dry weight and seed yield—At the end of the experiment, plant wereharvested and left to dry at 30° C. in a drying chamber. The vegetativeportion above ground was separated from the seeds. The total weight ofthe vegetative portion above ground and the seed weight of each plotwere measured and divided by the number of plants.

Dry weight (vegetative biomass)=total weight of the vegetative portionabove ground (excluding roots) after drying at 30° C. in a dryingchamber; all the above ground biomass that is not yield.

Seed yield per plant=total seed weight per plant (gr).

Harvest Index (seed)—The harvest index was calculated using Formula XVas described above.

T₅₀ days to flowering—Each of the repeats was monitored for floweringdate. Days of flowering was calculated from sowing date till 50% of theplots flowered.

Plant nitrogen level—The chlorophyll content of leaves is a goodindicator of the nitrogen plant status since the degree of leafgreenness is highly correlated to this parameter. Chlorophyll contentwas determined using a Minolta SPAD 502 chlorophyll meter andmeasurement was performed at time of flowering. SPAD meter readings weredone on young fully developed leaf. Three measurements per leaf weretaken per plot. Based on this measurement, parameters such as the ratiobetween seed yield per nitrogen unit [seed yield/N level=seed yield perplant [gr.]/SPAD unit], plant DW per nitrogen unit [DW/N level=plantbiomass per plant [gr.]/SPAD unit], and nitrogen level per gram ofbiomass [N level/DW=SPAD unit/plant biomass per plant (gr.)] werecalculated.

Percent of seed yield reduction—measures the amount of seeds obtained inplants when grown under nitrogen-limiting conditions compared to seedyield produced at normal nitrogen levels expressed in percentages (%).

Experimental Results

10 different Arabidopsis accessions (ecotypes) were grown andcharacterized for 34 parameters as described above. The average for eachof the measured parameters was calculated using the JMP software (Table55 below). Subsequent correlation analysis between the varioustranscriptome sets (Table 53) and the average parameters were conducted.

TABLE 55 Measured parameters in Arabidopsis accessions Ecotype/TreatmentLine-1 Line-2 Line-3 Line-4 Line-5 Line-6 Line-7 Line-8 Line-9 Line-10 10.02 0.02 0.02 0.01 0.02 0.01 0.01 0.02 0.02 0.02 2 60.75 76.71 78.5678.14 78.64 73.19 83.07 77.19 70.12 62.97 4 0.16 0.12 0.08 0.11 0.120.13 0.11 0.15 0.17 0.18 5 0.19 0.20 0.29 0.08 0.07 0.24 0.18 0.08 0.080.03 6 0.33 0.27 0.37 0.39 0.37 0.39 0.35 0.38 0.31 0.37 7 6.88 7.317.31 7.88 7.75 7.63 7.19 8.63 5.93 7.94 8 0.63 0.79 0.50 0.49 0.72 0.830.65 0.67 0.64 0.61 9 1.43 1.33 1.77 1.97 1.83 1.82 1.64 2.00 1.15 1.7510 0.76 0.71 1.06 1.16 1.00 0.91 0.94 1.12 0.64 1.00 12 0.03 0.03 0.020.01 0.01 0.03 0.02 0.01 0.01 0.01 13 72.56 84.70 78.78 88.00 92.6276.71 81.94 91.30 85.76 91.82 16 0.09 0.09 0.06 0.03 0.02 0.08 0.06 0.030.04 0.01 17 0.02 0.02 0.01 0.01 0.00 0.02 0.01 0.01 0.01 0.00 18 15.9720.97 14.84 24.71 23.70 18.06 19.49 23.57 21.89 23.57 21 0.01 0.02 0.020.01 0.02 0.02 0.01 0.02 0.02 0.02 22 0.42 0.53 0.38 0.52 0.58 0.50 0.630.65 0.57 0.50 23 0.28 0.31 0.28 0.16 0.21 0.28 0.17 0.21 0.17 0.14 240.34 0.31 0.52 0.45 0.43 0.50 0.43 0.51 0.41 0.43 25 6.25 7.31 8.06 8.758.75 8.38 7.13 9.44 6.31 8.06 26 0.69 1.02 0.61 0.60 0.65 0.68 0.58 0.610.52 0.48 27 1.41 1.57 2.67 2.42 2.14 2.47 1.97 2.72 1.64 2.21 28 0.760.86 1.48 1.28 1.10 1.24 1.09 1.41 0.89 1.22 29 0.12 0.17 0.11 0.08 0.120.14 0.11 0.14 0.09 0.07 31 0.08 0.11 0.04 0.03 0.06 0.06 0.06 0.05 0.060.03 32 0.34 0.53 0.21 0.18 0.28 0.28 0.25 0.27 0.24 0.16 34 16.37 20.5014.63 24.00 23.60 15.03 19.75 22.89 18.80 23.38 3 0.01 0.00 0.01 0.010.01 11 167.30 241.06 194.98 169.34 157.82 14 45.59 42.11 53.11 67.0028.15 15 0.00 0.00 0.00 0.00 0.00 19 0.02 0.02 0.02 0.01 0.03 20 22.4928.27 33.32 39.00 17.64 30 0.00 0.00 0.01 0.00 0.00 33 53.71 54.62 66.4868.05 35.55 Table 55. Provided are the measured parameters under varioustreatments in various ecotypes (Arabidopsis accessions).

TABLE 56 Correlation between the expression level of selected genes ofsome embodiments of the invention in various tissues and the phenotypicperformance under normal or abiotic stress conditions across Arabidopsisaccessions Gene Exp. Corr. Gene Exp. Corr. Name R P value set Set IDName R P value set Set ID LGP1 0.70 2.35E-02 2 34 LGP1 0.80 5.70E-03 118 LGP1 0.91 2.31E-04 1 34 LGP1 0.76 1.14E-02 1 13 LGP1 0.72 1.80E-02 328 LGP1 0.73 1.71E-02 3 5 LGP10 0.77 1.47E-02 4 21 LGP18 0.81 4.90E-03 22 LGP3 0.72 2.76E-02 4 28 LGP3 0.72 2.92E-02 4 7 LGP39 0.85 1.66E-03 218 LGP39 0.76 1.12E-02 2 34 LGP39 0.75 1.17E-02 2 13 LGP39 0.71 3.35E-024 7 LGP44 0.81 4.29E-03 2 18 LGP44 0.78 8.00E-03 2 13 LGP44 0.702.36E-02 2 22 LGP44 0.87 9.66E-04 3 18 LGP44 0.79 6.40E-03 3 34 LGP440.78 7.22E-03 3 13 LGP46 0.83 3.10E-03 2 18 LGP46 0.89 6.48E-04 2 34LGP46 0.92 1.84E-04 2 13 LGP46 0.85 1.68E-03 2 22 LGP46 0.71 3.39E-02 427 LGP46 0 .71 3.25E-02 4 9 LGP46 0.87 9.96E-04 1 18 LGP46 0.79 6.55E-031 34 LGP46 0.83 2.66E-03 1 13 LGP46 0.76 1.00E-02 1 1 LGP46 0.761.13E-02 3 34 LGP50 0.79 6.49E-03 2 18 LGP50 0.76 1.10E-02 2 34 LGP500.73 L64E-02 2 13 LGP50 0.72 1.92E-02 1 22 LGP53 0.80 8.99E-03 4 25LGP53 0.76 1.86E-02 4 28 LGP53 0.71 3.13E-02 4 10 LGP53 0.83 5.75E-03 47 LGP53 0.76 1.85E-02 4 27 LGP59 0.82 3.33E-03 2 2 LGP59 0.76 1.12E-02 15 LGP6 0.78 8.36E-03 1 17 LGP6 0.76 9.94E-03 1 16 LGP6 0.78 8.30E-03 112 LGP6 0.88 7.08E-04 1 5 LGP6 0.81 4.68E-03 3 23 LGP6 0.81 4.39E-03 312 LGP6 0.86 1.62E-03 3 5 LGP9 0.73 1.62E-02 2 17 LGP9 0.91 2.42E-04 231 LGP9 0.78 7.36E-03 2 16 LGP9 0.92 1.99E-04 2 32 LGP9 0.89 4.89E-04 226 LGP9 0.88 1.94E-03 4 25 LGP9 0.74 2.27E-02 4 7 LGP9 0.73 2.61E-02 427 LGP9 0.73 2.62E-02 4 9 LYD691 0.83 2.65E-03 2 21 LYD691 0.90 9.18E-044 21 LYD691 0.71 2.25E-02 1 21 LYD691 0.92 1.81E-04 3 21 Table 56. Table56. Provided are the correlations (R) between the expression levels ofyield improving genes and their homologues in tissues [Leaves or stems;Expression sets (Exp)] and the phenotypic performance in various yield,biomass, growth rate and/or vigor components [Correlation vector(corr.)] under nitrogen limiting conditions or normal conditions acrossArabidopsis accessions. “Corr. ID”—correlation set ID according to thecorrelated parameters specified in Table 54. “Exp. Set”—Expression setspecified in Table 53. “R” = Pearson correlation coefficient; “P” = pvalue.

Example 8 Production of Sorghum Transcriptome and High ThroughputCorrelation Analysis with ABST Related Parameters Using 44K SorghumOligonucleotide Micro-Arrays

In order to produce a high throughput correlation analysis between plantphenotype and gene expression level, the present inventors utilized asorghum oligonucleotide micro-array, produced by Agilent Technologies[chem. (dot) agilent (dot) com/Scripts/PDS (dot) asp?1Page=50879]. Thearray oligonucleotide represents about 44,000 sorghum genes andtranscripts. In order to define correlations between the levels of RNAexpression with ABST, yield and NUE components or vigor relatedparameters, various plant characteristics of 17 different sorghumhybrids were analyzed. Among them, 10 hybrids encompassing the observedvariance were selected for RNA expression analysis. The correlationbetween the RNA levels and the characterized parameters was analyzedusing Pearson correlation test [davidmlane (dot) com/hyperstat/A34739(dot) html].

I. Correlation of Sorghum Varieties Across Ecotypes Grown Under RegularGrowth Conditions, Severe Drought Conditions and Low Nitrogen Conditions

Experimental Procedures

17 Sorghum varieties were grown in 3 repetitive plots, in field.Briefly, the growing protocol was as follows:

1. Regular growth conditions: sorghum plants were grown in the fieldusing commercial fertilization and irrigation protocols (370,000 literper dunam (1000 square meters), fertilization of 14 units of nitrogenper dunam entire growth period).

2. Drought conditions: sorghum seeds were sown in soil and grown undernormal condition until around 35 days from sowing, around stage V8(eight green leaves are fully expanded, booting not started yet). Atthis point, irrigation was stopped, and severe drought stress wasdeveloped.

3. Low Nitrogen fertilization conditions: sorghum plants were fertilizedwith 50% less amount of nitrogen in the field than the amount ofnitrogen applied in the regular growth treatment. All the fertilizer wasapplied before flowering.

Analyzed Sorghum tissues—All 10 selected Sorghum hybrids were sampledper each treatment. Tissues [Flag leaf, Flower meristem and Flower] fromplants growing under normal conditions, severe drought stress and lownitrogen conditions were sampled and RNA was extracted as describedabove. Each micro-array expression information tissue type has receiveda Set ID as summarized in Table 57 below.

TABLE 57 Sorghum transcriptome expression sets Expression Set Set IDFlag leaf at flowering stage under drought growth conditions 1 Flag leafat flowering stage under low nitrogen growth 2 conditions Flag leaf atflowering stage under normal growth conditions 3 Flower meristem atflowering stage under drought growth 4 conditions Flower meristem atflowering stage under low nitrogen 5 growth conditions Flower meristemat flowering stage under normal growth 6 conditions Flower at floweringstage under drought growth conditions 7 Flower at flowering stage underlow nitrogen growth conditions 8 Flower at flowering stage under normalgrowth conditions 9 Table 57: Provided are the sorghum transcriptomeexpression sets 1-9. Flag leaf = the leaf below the flower; Flowermeristem = Apical meristem following panicle initiation; Flower = theflower at the anthesis day. Expression sets 3, 6, and 9 are from plantsgrown under normal conditions; Expression sets 2, 5 and 8 are fromplants grown under Nitrogen-limiting conditions; Expression sets 1, 4and 7 are from plants grown under drought conditions.

The following parameters were collected using digital imaging system:

At the end of the growing period the grains were separated from thePlant ‘Head’ and the following parameters were measured and collected:

Average Grain Area (cm²)—A sample of ˜200 grains was weighted,photographed and images were processed using the below described imageprocessing system. The grain area was measured from those images and wasdivided by the number of grains.

Upper and Lower Ratio Average of Grain Area, width, length, diameter andperimeter—Grain projection of area, width, diameter and perimeter wereextracted from the digital images using open source package imagej(nih). Seed data was analyzed in plot average levels as follows:

Average of all seeds;

Average of upper 20% fraction—contained upper 20% fraction of seeds;

Average of lower 20% fraction—contained lower 20% fraction of seeds;

Further on, ratio between each fraction and the plot average wascalculated for each of the data parameters.

At the end of the growing period 5 ‘Heads’ were photographed and imageswere processed using the below described image processing system.

(i) Head Average Area (cm²)—At the end of the growing period 5 ‘Heads’were photographed and images were processed using the below describedimage processing system. The ‘Head’ area was measured from those imagesand was divided by the number of ‘Heads’.

(ii) Head Average Length (cm)—At the end of the growing period 5 ‘Heads’were photographed and images were processed using the below describedimage processing system. The ‘Head’ length (longest axis) was measuredfrom those images and was divided by the number of ‘Heads’.

(iii) Head Average width (cm)—At the end of the growing period 5 ‘Heads’were photographed and images were processed using the below describedimage processing system. The ‘Head’ width was measured from those imagesand was divided by the number of ‘Heads’.

(iv) Head Average perimeter (cm)—At the end of the growing period 5‘Heads’ were photographed and images were processed using the belowdescribed image processing system. The ‘Head’ perimeter was measuredfrom those images and was divided by the number of ‘Heads’.

The image processing system was used, which consists of a personaldesktop computer (Intel P4 3.0 GHz processor) and a public domainprogram—ImageJ 1.37, Java based image processing software, which wasdeveloped at the U.S. National Institutes of Health and is freelyavailable on the internet at rsbweb (dot) nih (dot) gov/. Images werecaptured in resolution of 10 Mega Pixels (3888×2592 pixels) and storedin a low compression JPEG (Joint Photographic Experts Group standard)format. Next, image processing output data for seed area and seed lengthwas saved to text files and analyzed using the JMP statistical analysissoftware (SAS institute).

Additional parameters were collected either by sampling 5 plants perplot or by measuring the parameter across all the plants within theplot.

Total Grain Weight/Head (gr.) (grain yield)—At the end of the experiment(plant ‘Heads’) heads from plots within blocks A-C were collected. 5heads were separately threshed and grains were weighted, all additionalheads were threshed together and weighted as well. The average grainweight per head was calculated by dividing the total grain weight bynumber of total heads per plot (based on plot). In case of 5 heads, thetotal grains weight of 5 heads was divided by 5.

FW Head/Plant gram—At the end of the experiment (when heads wereharvested) total and 5 selected heads per plots within blocks A-C werecollected separately. The heads (total and 5) were weighted (gr.)separately and the average fresh weight per plant was calculated fortotal (FW Head/Plant gr. based on plot) and for 5 (FW Head/Plant gr.based on 5 plants) plants.

Plant height—Plants were characterized for height during growing periodat 5 time points. In each measure, plants were measured for their heightusing a measuring tape. Height was measured from ground level to top ofthe longest leaf.

SPAD—Chlorophyll content was determined using a Minolta SPAD 502chlorophyll meter and measurement was performed 64 days post sowing.SPAD meter readings were done on young fully developed leaf. Threemeasurements per leaf were taken per plot.

Vegetative fresh weight and Heads—At the end of the experiment (whenInflorescence were dry) all Inflorescence and vegetative material fromplots within blocks A-C were collected. The biomass and Heads weight ofeach plot was separated, measured and divided by the number of Heads.

Plant biomass (Fresh weight)—At the end of the experiment (whenInflorescence were dry) the vegetative material from plots within blocksA-C were collected. The plants biomass without the Inflorescence weremeasured and divided by the number of Plants.

FW Heads/(FW Heads+FW Plants)—The total fresh weight of heads and theirrespective plant biomass were measured at the harvest day. The headsweight was divided by the sum of weights of heads and plants.

Experimental Results

17 different sorghum varieties were grown and characterized fordifferent parameters: The average for each of the measured parameterswas calculated using the JMP software (Tables 59-60) and a subsequentcorrelation analysis between the various transcriptome sets (Table 57)and the average parameters, was conducted (Table 61). Results were thenintegrated to the database.

TABLE 58 Sorghum correlated parameters (vectors) Correlation Correlatedparameter with ID Average Grain Area (cm²), Drought 1 Average Grain Area(cm²), Low N 2 Average Grain Area (cm²), Normal 3 FW - Head/Plant (gr)(based on plot), Drought 4 FW - Head/Plant (gr.) (based on plot), Low N5 FW - Head/Plant (gr.) (based on plot), Normal 6 FW - Head/Plant (gr.)(based on 5 plants), Low N 7 FW - Head/Plant (gr.) (based on 5 plants),Normal 8 FW Heads/(FW Heads + FW Plants)(all plot), Drought 9 FWHeads/(FW Heads + FW Plants)(all plot), Low N 10 FW Heads/(FW Heads + FWPlants) (all plot), Normal 11 FW/Plant (gr) (based on plot), Drought 12FW/Plant (gr.) (based on plot), Low N 13 FW/Plant (gr.) (based on plot),Normal 14 Final Plant Height (cm), Drought 15 Final Plant Height (cm),Low N 16 Final Plant Height (cm), Normal 17 Head Average Area (cm²),Drought 18 Head Average Area (cm²), Low N 19 Head Average Area (cm²),Normal 20 Head Average Length (cm), Drought 21 Head Average Length (cm),Low N 22 Head Average Length (cm), Normal 23 Head Average Perimeter(cm), Drought 24 Head Average Perimeter (cm), Low N 25 Head AveragePerimeter (cm), Normal 26 Head Average Width (cm), Drought 27 HeadAverage Width (cm), Low N 28 Head Average Width (cm), Normal 29 LeafSPAD 64 DPS (Days Post Sowing), Drought 30 Leaf SPAD 64 DPS (Days PostSowing), Low N 31 Leaf SPAD 64 DPS (Days Post Sowing), Normal 32 LowerRatio Average Grain Area (value), Low N 33 Lower Ratio Average GrainArea (value), Normal 34 Lower Ratio Average Grain Length (value), Low N35 Lower Ratio Average Grain Length (value), Normal 36 Lower RatioAverage Grain Perimeter (value), Low N 37 Lower Ratio Average GrainPerimeter, (value) Normal 38 Lower Ratio Average Grain Width (value),Low N 39 Lower Ratio Average Grain Width (value), Normal 40 Total grainweight/Head (based on plot) (gr.), Low N 41 Total grain weight/Head(gr.) (based on 5 heads), Low N 42 Total grain weight/Head (gr.) (basedon 5 heads), Normal 43 Total grain weight/Head (gr.) (based on plot),Normal 44 Total grain weight/Head (gr.) (based on plot), Drought 45Upper Ratio Average Grain Area, Drought (value) 46 Upper Ratio AverageGrain Area (value), Low N 47 Upper Ratio Average Grain Area (value),Normal 48 [Grain Yield + plant biomass/SPAD 64 DPS] (gr.), Normal 49[Grain Yield + plant biomass/SPAD 64 DPS] (gr.), Low N 50 [Grainyield/SPAD 64 DPS] (gr.), Low N 51 [Grain yield/SPAD 64 DPS] (gr.),Normal 52 [Plant biomass (FW)/SPAD 64 DPS] (gr) Drought 53 [Plantbiomass (FW)/SPAD 64 DPS] (gr.), Low N 54 Table 58. Provided are theSorghum correlated parameters (vectors). “gr.” = grams; “SPAD” =chlorophyll levels; “FW” = Plant Fresh weight; “normal” = standardgrowth conditions.

TABLE 59 Measured parameters in Sorghum accessions Ecotype/TreatmentLine-1 Line-2 Line-3 Line-4 Line-5 Line-6 Line-7 Line-8 Line-9 1 0.100.11 0.11 0.09 0.09 0.11 2 0.11 0.11 0.14 0.12 0.14 0.13 0.12 0.12 0.123 0.105 0.112 0.131 0.129 0.139 0.141 0.110 0.113 0.102 4 154.90 122.02130.51 241.11 69.03 186.41 62.11 39.02 58.94 5 214.78 205.05 73.49122.96 153.07 93.23 134.11 77.43 129.63 6 175.15 223.49 56.40 111.6267.34 66.90 126.18 107.74 123.86 7 388.00 428.67 297.67 280.00 208.33303.67 436.00 376.33 474.67 8 406.50 518.00 148.00 423.00 92.00 101.33423.50 386.50 409.50 9 0.42 0.47 0.42 0.37 0.23 0.31 0.41 0.44 0.40 100.51 0.51 0.17 0.39 0.21 0.19 0.48 0.37 0.42 11 0.51 0.51 0.12 0.26 0.120.18 0.46 0.43 0.42 12 207.99 138.02 255.41 402.22 233.55 391.75 89.3150.61 87.02 13 204.78 199.64 340.51 240.60 537.78 359.40 149.20 129.06178.71 14 162.56 212.59 334.83 313.46 462.28 318.26 151.13 137.60 167.9815 89.40 75.73 92.10 94.30 150.80 110.73 99.20 84.00 99.00 16 104.0080.93 204.73 125.40 225.40 208.07 121.40 100.27 121.13 17 95.25 79.20197.85 234.20 189.40 194.67 117.25 92.80 112.65 18 83.14 107.79 88.68135.91 90.76 123.95 86.06 85.20 113.10 19 96.24 214.72 98.59 182.83119.64 110.19 172.36 84.81 156.25 20 120.14 167.60 85.14 157.26 104.00102.48 168.54 109.32 135.13 21 21.63 21.94 21.57 22.01 20.99 28.60 21.3520.81 24.68 22 23.22 25.58 20.93 28.43 24.32 22.63 32.11 20.38 26.69 2325.58 26.84 21.02 26.84 23.14 21.82 31.33 23.18 25.70 24 52.78 64.4956.59 64.37 53.21 71.66 55.61 52.96 69.83 25 56.32 79.20 53.25 76.2167.27 59.49 79.28 51.52 69.88 26 61.22 67.90 56.26 65.38 67.46 67.4674.35 56.16 61.64 27 4.83 6.31 5.16 7.78 5.28 5.49 5.04 5.07 5.77 285.26 10.41 5.93 8.25 6.19 6.12 6.80 5.25 7.52 29 5.97 7.92 4.87 7.435.58 5.88 6.78 5.99 6.62 30 40.58 40.88 45.01 42.30 45.24 40.56 44.8045.07 40.65 31 38.33 38.98 42.33 40.90 43.15 39.85 42.68 43.31 39.01 3243.01 . 43.26 44.74 45.76 41.61 45.21 45.14 43.03 33 0.82 0.77 0.81 0.790.78 0.80 0.83 0.79 0.81 34 0.825 0.740 0.778 0.802 0.697 0.699 0.8270.805 0.841 35 0.91 0.90 0.92 0.90 0.91 0.93 0.92 0.89 0.90 36 0.9140.884 0.921 0.908 0.890 0.877 0.913 0.903 0.920 37 0.90 0.88 0.92 0.900.92 0.92 0.92 0.89 0.90 38 0.91 0.87 0.91 0.95 0.90 0.91 0.91 0.91 0.9239 0.90 0.85 0.89 0.88 0.86 0.87 0.91 0.89 0.90 40 0.91 0.83 0.85 0.870.79 0.80 0.90 0.89 0.91 41 25.95 30.57 19.37 35.62 25.18 22.18 49.9627.48 51.12 42 50.27 50.93 36.13 73.10 37.87 36.40 71.67 35.00 76.73 4347.40 46.30 28.37 70.40 32.15 49.23 63.45 44.45 56.65 44 31.12 26.3518.72 38.38 26.67 28.84 47.67 31.00 39.99 45 22.11 16.77 9.19 104.443.24 22.00 9.97 18.58 29.27 46 1.31 1.19 1.29 1.46 1.21 1.21 47 1.181.31 1.11 1.21 1.19 1.18 1.16 1.23 1.17 48 1.22 1.30 1.13 1.14 1.16 1.151.19 1.23 1.25 49 4.50 8.17 7.87 10.68 8.34 4.40 3.74 4.83 3.67 50 6.025.91 8.50 6.75 13.05 9.58 4.67 3.61 5.89 51 0.68 0.78 0.46 0.87 0.580.56 1.17 0.63 1.31 52 3.78 7.74 7.01 10.10 7.65 3.34 3.05 3.90 2.83 535.13 3.38 5.67 9.51 5.16 9.66 1.99 1.12 2.14 54 5.34 5.12 8.05 5.8812.46 9.02 3.50 2.98 4.58 55 0.72 0.43 0.86 0.58 0.69 1.05 0.69 0.930.84 Table 59: Provided are the values of each of the parameters (asdescribed above) measured in Sorghum accessions (ecotype) under normal,low nitrogen and drought conditions. Growth conditions are specified inthe experimental procedure section.

TABLE 60 Additional measured parameters in Sorghum accessionsEcotype/Treatment Line-10 Line-11 Line-12 Line-13 Line-14 Line-15Line-16 Line-17 1 2 0.13 0.13 0.12 0.12 0.11 0.11 0.12 0.11 3 0.1180.121 0.111 0.117 0.108 0.105 0.110 0.105 4 76.37 33.47 42.20 41.53131.67 60.84 44.33 185.44 5 99.83 76.95 84.25 92.24 138.83 113.32 95.50129.49 6 102.75 82.33 77.59 91.17 150.44 109.10 107.58 130.88 7 437.67383.00 375.00 425.00 434.00 408.67 378.50 432.00 8 328.95 391.00 435.75429.50 441.00 415.75 429.50 428.50 9 0.44 0.47 0.47 0.48 0.35 0.35 0.230.33 10 0.44 0.43 0.39 0.44 0.44 0.44 0.43 0.42 11 0.44 0.46 0.45 0.450.51 0.46 0.44 0.39 12 120.43 37.21 48.18 44.20 231.60 116.01 123.08342.50 13 124.27 101.33 132.12 117.90 176.99 143.67 126.98 180.45 14128.97 97.62 99.32 112.24 157.42 130.55 135.66 209.21 15 92.20 81.9398.80 86.47 99.60 83.00 83.53 92.30 16 94.53 110.00 115.07 104.73 173.67115.60 138.80 144.40 17 97.50 98.00 100.00 105.60 151.15 117.10 124.45126.50 18 100.79 80.41 126.89 86.41 92.29 77.89 76.93 19 136.71 137.7096.54 158.19 163.95 138.39 135.46 165.64 20 169.03 156.10 112.14 154.74171.70 168.51 162.51 170.46 21 24.28 21.95 24.98 19.49 20.42 16.81 18.8822 26.31 25.43 23.11 27.87 28.88 27.64 25.52 30.33 23 28.82 28.13 22.9728.09 30.00 30.54 27.17 29.26 24 65.14 55.27 69.06 53.32 56.29 49.1251.88 25 66.17 67.37 57.90 70.61 73.76 66.87 65.40 75.97 26 71.40 68.5656.44 67.79 71.54 78.94 67.03 74.11 27 5.37 4.66 6.35 5.58 5.76 5.865.10 28 6.59 6.85 5.32 7.25 7.19 6.27 6.57 6.82 29 7.42 6.98 6.19 7.027.18 7.00 7.39 7.35 30 45.43 42.58 44.18 44.60 42.41 43.25 40.30 40.7531 42.71 40.08 43.98 45.44 44.75 42.58 43.81 46.73 32 45.59 44.83 45.3346.54 43.99 45.09 45.14 43.13 33 0.77 0.74 0.80 0.79 0.82 0.80 0.81 0.8134 0.788 0.765 0.803 0.806 0.821 0.814 0.818 0.817 35 0.91 0.89 0.900.89 0.91 0.89 0.89 0.90 36 0.923 0.893 0.913 0.907 0.911 0.904 0.9030.913 37 0.91 0.89 0.90 0.90 0.91 0.89 0.90 0.90 38 0.93 0.91 0.92 0.900.91 0.90 0.91 0.91 39 0.86 0.84 0.90 0.89 0.91 0.90 0.90 0.90 40 0.850.86 0.88 0.90 0.90 0.91 0.90 0.90 41 36.84 29.45 26.70 29.42 51.1237.04 39.85 41.78 42 57.58 42.93 36.47 68.60 71.80 49.27 43.87 52.07 4360.00 45.45 58.19 70.60 70.10 53.95 59.87 52.65 44 38.36 32.10 32.6932.79 51.53 35.71 38.31 42.44 45 10.45 14.77 12.86 18.24 11.60 18.6516.36 46 47 1.22 1.24 1.19 1.23 1.16 1.34 1.21 1.21 48 1.24 1.32 1.221.18 1.18 1.22 1.25 1.22 49 2.89 2.91 3.12 4.75 3.69 3.85 5.84 50 3.773.26 3.61 3.24 5.10 4.25 3.81 4.76 51 0.86 0.73 0.61 0.65 1.14 0.87 0.910.89 52 2.18 2.19 2.41 3.58 2.90 3.01 4.85 53 2.65 0.87 1.09 0.99 5.462.68 3.05 8.40 54 2.91 2.53 3.00 2.60 3.96 3.38 2.90 3.86 55 0.72 0.720.70 1.17 0.79 0.85 0.98 Table 60: Provided are the values of each ofthe parameters (as described above) measured in Sorghum accessions(ecotype) under normal, low nitrogen and drought conditions. Growthconditions are specified in the experimental procedure section.

TABLE 61 Correlation between the expression level of selected genes ofsome embodiments of the invention in various tissues and the phenotypicperformance under normal or abiotic stress conditions across Sorghumaccessions Gene Exp. Corr. Gene Exp. Corr. Name R P value set Set IDName R P value set Set ID LGP102 0.75 1.27E−02 6 17 LGP102 0.70 2.42E−026 20 LGP102 0.87 1.10E−03 4 53 LGP102 0.86 1.50E−03 4 4 LGP102 0.879.79E−04 4 12 LGP52 0.71 2.13E−02 6 17 LGP52 0.78 7.56E−03 6 44 LGP520.74 1.48E−02 6 36 MGP7 0.76 1.06E−02 9 17 Table 61. Provided are thecorrelations (R) between the expression levels of yield improving genesand their homologues in tissues [Flag leaf, Flower meristem, stem andFlower; Expression sets (Exp)] and the phenotypic performance in variousyield, biomass, growth rate and/or vigor components [Correlation vector(corr.)] under stress conditions or normal conditions across Sorghumaccessions. P = p value.

II. Correlation of Sorghum Varieties Across Ecotype Grown Under SalinityStress and Cold Stress Conditions

Sorghum vigor related parameters under 100 mM NaCl and low temperature(10±2° C.)—Ten Sorghum varieties were grown in 3 repetitive plots, eachcontaining 17 plants, at a net house under semi-hydroponics conditions.Briefly, the growing protocol was as follows: Sorghum seeds were sown intrays filled with a mix of vermiculite and peat in a 1:1 ratio.Following germination, the trays were transferred to the high salinitysolution (100 mM NaCl in addition to the Full Hogland solution), lowtemperature (10±2° C. in the presence of Full Hogland solution) or atNormal growth solution [Full Hogland solution at 28±2° C.].

Full Hogland solution consists of: KNO₃—0.808 grams/liter, MgSO₄—0.12grams/liter, KH₂PO₄—0.172 grams/liter and 0.01% (volume/volume) of‘Super coratin’ micro elements (Iron-EDDHA[ethylenediamine-N,N′-bis(2-hydroxyphenyl acetic acid)]—40.5grams/liter; Mn—20.2 grams/liter; Zn 10.1 grams/liter; Co 1.5grams/liter; and Mo 1.1 grams/liter), solution's pH should be 6.5-6.8].

All 10 selected varieties were sampled per each treatment. Two tissues[leaves and roots] growing at 100 mM NaCl, low temperature (10±2° C.) orunder Normal conditions (full Hogland at a temperature between 28±2° C.)were sampled and RNA was extracted as described hereinabove under“GENERAL EXPERIMENTAL AND BIOINFORMATICS METHODS”.

TABLE 62 Sorghum transcriptome expression sets Expression Set Set IDroot at vegetative stage (V4-V5) under cold conditions 1 root vegetativestage (V4-V5) under normal conditions 2 root vegetative stage (V4-V5)under low nitrogen conditions 3 root vegetative stage (V4-V5) undersalinity conditions 4 vegetative meristem at vegetative stage (V4-V5)under 5 cold conditions vegetative meristem at vegetative stage (V4-V5)under low 6 nitrogen conditions vegetative meristem at vegetative stage(V4-V5) under 7 salinity conditions vegetative meristem at vegetativestage (V4-V5) under 8 normal conditions Table 62: Provided are theSorghum transcriptome expression sets. Cold conditions = 10 ± 2° C.;NaCl = 100 mM NaCl; low nitrogen = 1.2 mM Nitrogen; Normal conditions =16 mM Nitrogen.

Sorghum Biomass, Vigor, Nitrogen Use Efficiency and Growth-RelatedComponents

Root DW (dry weight)—At the end of the experiment, the root material wascollected, measured and divided by the number of plants.

Shoot DW—At the end of the experiment, the shoot material (withoutroots) was collected, measured and divided by the number of plants.

Total biomass—total biomass including roots and shoots.

Plant leaf number—Plants were characterized for leaf number at 3 timepoints during the growing period. In each measure, plants were measuredfor their leaf number by counting all the leaves of 3 selected plantsper plot.

Shoot/root Ratio—The shoot/root Ratio was calculated using Formula XXXabove.

Percent of reduction of root biomass compared to normal—the difference(reduction in percent) between root biomass under normal and under lownitrogen conditions.

Percent of reduction of shoot biomass compared to normal—the difference(reduction in percent) between shoot biomass under normal and under lownitrogen conditions.

Percent of reduction of total biomass compared to normal—the difference(reduction in percent) between total biomass (shoot and root) undernormal and under low nitrogen conditions

Plant height—Plants were characterized for height at 3 time pointsduring the growing period. In each measure, plants were measured fortheir height using a measuring tape. Height was measured from groundlevel to top of the longest leaf

Relative Growth Rate of leaf number was calculated using Formula VIIIabove.

SPAD—Chlorophyll content was determined using a Minolta SPAD 502chlorophyll meter and measurement was performed 64 days post sowing.SPAD meter readings were done on young fully developed leaf. Threemeasurements per leaf were taken per plot.

Root Biomass [DW-gr.]/SPAD—root biomass divided by SPAD results.

Shoot Biomass [DW-gr.]/SPAD—shoot biomass divided by SPAD results.

Total Biomass-Root+Shoot [DW-gr.]/SPAD—total biomass divided by SPADresults.

Plant nitrogen level—calculated as SPAD/leaf biomass—The chlorophyllcontent of leaves is a good indicator of the nitrogen plant status sincethe degree of leaf greenness is highly correlated to this parameter.

Experimental Results

10 different Sorghum varieties were grown and characterized for thefollowing parameters: “Leaf number Normal”=leaf number per plant undernormal conditions (average of five plants); “Plant Height Normal”=plantheight under normal conditions (average of five plants); “Root DW 100 mMNaCl”—root dry weight per plant under salinity conditions (average offive plants); The average for each of the measured parameters wascalculated using the JMP software and values are summarized in Table 64below. Subsequent correlation analysis between the various transcriptomesets and the average parameters were conducted (Table 65). Results werethen integrated to the database.

TABLE 63 Sorghum correlated parameters (vectors) Corre- lationCorrelated parameter with ID DW Root/Plant (gr./number)- 100 mM NaCl 1DW Root/Plant, (gr/number) under Cold 2 DW Root/Plant (gr./number) atLow Nitrogen 3 DW Root/Plant (gr/number) - Normal 4 DW Shoot/Plant(gr./number) at Low Nitrogen 5 DW Shoot/Plant (gr./number) - 100 mM NaCl6 DW Shoot/Plant, (gr/number) under Cold 7 DW Shoot/Plant (gr/number) -Normal 8 Leaf number (at time point 1), under 100 mM NaCl 9 Leaf number(at time point 1), under Cold 10 Leaf number (at time point 1), [LowNitrogen] 11 Leaf number (at time point 1), under Normal 12 Leaf number(at time point 2), under 100 mM NaCl 13 Leaf number (at time point 2),under Cold 14 Leaf number (at time point 2), [Low Nitrogen] 15 Leafnumber (at time point 2), under Normal 16 Leaf number (at time point 3),under 100 mM NaCl 17 Leaf number (at time point 3), under Cold 18 Leafnumber (at time point 3), [Low Nitrogen] 19 Leaf number (at time point3), under Normal 20 Low N - total biomass DW (gr.) 21 Low N - Shoot/Root(ratio) 22 Low N (low nitrogen) roots DW (gr.) 23 Low N (low nitrogen)shoots DW (gr.) 24 Low N percent root biomass compared to normal 25 LowN percent shoot biomass compared to normal 26 Low N percent totalbiomass reduction compared to normal 27 N level/Leaf (SPAD/gr) [LowNitrogen] 28 N level/Leaf (SPAD/gr) [100 mM NaCl] 29 N level/Leaf(SPAD/gr) [Cold] 30 N level/Leaf (SPAD/gr) [Normal] 31 Normal,Shoot/Root (ratio) 32 Roots DW (gr) [normal] 33 Shoots DW (gr) [normal]34 Total biomass (gr) [normal] 35 Plant Height (at time point 1),(cm)[100 mM NaCl] 36 Plant Height (at time point 1), (cm) under Cold 37Plant Height (at time point 1), (cm)[Low Nitrogen] 38 Plant Height (attime point 1), (cm) [normal] 39 Plant Height (at time point 2), (cm)under Cold 40 Plant Height (at time point 2), (cm)[Low Nitrogen] 41Plant Height (at time point 2), (cm) [normal] 42 Plant Height (at timepoint 2), (cm)[100 mM NaCl] 43 Plant Height (at time point 3), (cm) [100mM NaCl] 44 Plant Height (at time point 3), (cm) [Low Nitrogen] 45 RGRLeaf Num Normal 46 Root Biomass (DW - gr.)/SPAD [100 mM NaCl] 47 RootBiomass (DW, gr.)/SPAD [Cold] 48 Root Biomass (DW, gr.)/SPAD [LowNitrogen] 49 Root Biomass [DW, gr.]/SPAD [Normal] 50 SPAD, underCold 51SPAD (number) at Low Nitrogen 52 SPAD (number) - Normal 53 SPAD at 100mM NaCl (number) 54 Shoot Biomass (DW, gr.)/SPAD [100 mM NaCl] 55 ShootBiomass (DW, gr.)/SPAD [Cold] 56 Shoot Biomass (DW, gr.)/SPAD [LowNitrogen] 57 Shoot Biomass (DW, gr.)/SPAD [Normal] 58 Total Biomass(Root + Shoot; DW, gr.)/SPAD [100 mM NaCl] 59 Total Biomass (Root +Shoot; DW, gr.)/SPAD [Cold] 60 Total Biomass (Root + Shoot; DW,gr.)/SPAD [Low Nitrogen] 61 Total Biomass (Root + Shoot; DW, gr.)/SPAD[Normal] 62 Table 63: Provided are the Sorghum correlated parameters.Cold conditions = 10 ± 2° C.; NaCl = 100 mM NaCl; low nitrogen = 1.2 mMNitrogen; Normal conditions = 16 mM Nitrogen.

TABLE 64 Sorghum accessions, measured parameters Ecotype/ Line-Treatment Line-1 Line-2 Line-3 Line-4 Line-5 Line-6 Line-7 Line-8 Line-910 4 0.05 0.13 0.17 0.10 0.11 0.12 0.14 0.12 0.10 0.11 8 0.10 0.24 0.310.16 0.19 0.19 0.24 0.24 0.19 0.24 12 3.00 3.07 3.80 3.20 3.23 3.23 3.133.43 3.00 3.00 16 4.17 4.50 4.80 4.60 4.53 4.97 4.60 4.93 4.50 4.57 205.33 5.87 6.20 5.80 5.80 5.73 5.73 6.00 5.60 6.07 39 7.47 9.30 12.878.57 8.93 8.53 10.67 10.27 7.87 8.77 42 14.97 18.23 22.10 17.60 18.0718.53 22.83 22.03 20.03 21.80 46 0.16 0.19 0.16 0.17 0.17 0.17 0.17 0.170.17 0.20 53 26.70 29.33 29.86 29.09 24.98 24.62 30.79 25.50 32.89 33.543 0.04 0.11 0.20 0.10 0.08 0.09 0.13 0.09 0.09 0.09 5 0.08 0.19 0.330.16 0.16 0.16 0.26 0.20 0.13 0.18 11 3.00 3.13 3.87 3.53 3.20 3.13 3.133.30 3.07 3.07 15 4.00 4.58 4.97 4.73 4.60 4.70 4.97 4.87 4.67 4.57 193.90 4.27 4.70 4.23 4.30 4.57 4.63 4.67 3.97 4.10 38 6.73 9.77 12.708.67 9.77 9.23 10.27 10.10 7.93 8.23 41 13.30 20.63 23.70 18.03 19.3319.20 21.87 22.13 18.20 21.00 45 22.23 31.07 34.67 30.03 30.83 29.8730.87 32.40 29.37 30.70 52 26.88 28.02 29.64 31.52 29.61 26.82 28.4828.21 30.48 27.63 1 0.05 0.10 0.12 0.07 0.08 0.08 0.14 0.10 0.16 0.14 60.09 0.19 0.20 0.14 0.13 0.13 0.15 0.19 0.10 0.12 9 3.00 3.13 3.40 3.073.33 3.07 3.07 3.27 3.00 3.07 13 4.00 4.37 4.87 4.60 4.50 4.53 4.50 4.774.32 4.20 17 4.00 4.13 4.57 4.43 4.07 4.33 4.13 4.50 3.78 4.20 36 7.909.50 10.93 7.93 9.70 8.53 8.90 10.37 7.00 7.83 43 14.20 16.27 20.3713.33 15.90 16.53 15.47 18.93 13.68 15.77 44 21.80 23.17 30.37 22.8323.70 23.30 22.47 26.83 20.28 23.57 54 32.73 35.14 27.97 30.93 34.5329.99 32.09 31.86 32.51 34.32 2 0.07 0.11 0.16 0.09 0.08 0.11 0.14 0.130.11 0.14 7 0.08 0.15 0.19 0.11 0.13 0.16 0.15 0.15 0.11 0.14 10 3.003.00 3.50 3.17 3.40 3.20 3.13 3.07 3.07 3.00 14 3.90 4.13 4.63 4.17 4.274.23 4.20 4.30 4.17 4.00 18 4.73 5.33 5.43 5.50 5.33 5.07 4.50 5.40 5.375.18 37 6.50 8.77 10.40 6.80 9.03 9.00 7.97 9.17 6.50 7.23 40 11.1715.87 18.43 12.20 16.03 14.63 14.60 17.27 13.43 13.91 51 28.62 30.3127.04 32.28 28.28 29.89 32.47 28.63 31.71 29.56 30 6.05 5.68 4.98 5.875.30 5.90 7.21 5.30 5.91 5.70 48 0.002 0.004 0.006 0.003 0.003 0.0040.004 0.004 0.003 0.005 56 0.003 0.005 0.007 0.003 0.005 0.006 0.0050.005 0.004 0.005 60 0.005 0.009 0.013 0.006 0.008 0.009 0.009 0.0100.007 0.009 21 27.53 64.12 115.23 58.02 52.22 35.10 84.57 63.73 47.0360.00 22 1.87 1.71 1.73 1.57 2.10 1.81 2.06 2.10 1.50 2.00 23 9.65 23.5443.88 22.58 16.89 12.44 28.19 20.53 18.76 20.09 24 17.88 40.59 71.3535.44 35.33 22.66 56.38 43.20 28.27 39.91 25 84.53 80.95 117.00 100.5272.54 71.78 93.47 76.05 86.82 80.51 26 81.57 79.16 104.75 103.50 83.7183.22 107.69 81.39 70.30 75.86 27 82.58 79.81 109.10 102.32 79.74 78.77102.49 79.59 76.07 77.36 28 6.89 6.57 6.31 7.45 6.89 5.87 6.15 6.05 7.686.74 49 0.002 0.004 0.007 0.003 0.003 0.003 0.005 0.003 0.003 0.003 570.003 0.007 0.011 0.005 0.005 0.006 0.009 0.007 0.004 0.007 61 0.0050.011 0.018 0.008 0.008 0.009 0.014 0.010 0.007 0.010 29 8.18 8.50 6.126.98 8.49 6.92 7.76 7.08 8.60 8.17 47 0.002 0.003 0.004 0.002 0.0020.003 0.004 0.003 0.005 0.004 55 0.003 0.005 0.007 0.004 0.004 0.0040.005 0.006 0.003 0.004 59 0.004 0.008 0.012 0.007 0.006 0.007 0.0090.009 0.008 0.008 31 5.01 5.00 4.82 5.02 4.31 4.29 5.37 4.25 5.87 5.5332 1.98 1.94 1.90 1.59 1.81 1.58 1.76 1.99 1.89 2.20 33 0.86 2.19 2.831.69 1.76 1.96 2.27 2.04 1.09 1.88 34 1.65 3.87 5.14 2.58 3.18 3.08 3.954.00 2.02 3.97 35 2.51 6.06 7.96 4.28 4.94 5.04 6.22 6.04 3.11 5.85 500.002 0.005 0.006 0.004 0.004 0.005 0.005 0.005 0.003 0.003 58 0.0040.008 0.010 0.005 0.008 0.008 0.008 0.010 0.006 0.007 62 0.006 0.0130.016 0.009 0.012 0.012 0.012 0.014 0.009 0.011 Table 64: Provided arethe measured parameters under 100 mM NaCl and low temperature (8-10° C.)conditions of Sorghum accessions (Seed ID) according to the CorrelationID numbers (described in Table 63 above).

TABLE 65 Correlation between the expression level of selected genes ofsome embodiments of the invention in roots and the phenotypicperformance under normal or abiotic stress conditions across Sorghumaccessions Corr. Gene Exp. Set Gene Exp. Corr. Name R P value set IDName R P value set Set ID LGP102 0.79 1.10E−02 6 52 LGP52 0.76 4.65E−023 15 LGP52 0.71 7.55E−02 3 45 LGP52 0.72 7.05E−02 3 38 LGP52 0.742.14E−02 5 7 LGP52 0.84 4.64E−03 5 48 LGP52 0.80 9.65E−03 5 2 LGP52 0.771.54E−02 5 56 LGP52 0.83 6.12E−03 5 60 LGP52 0.79 1.17E−02 5 14 LGP520.87 2.45E−03 6 49 LGP52 0.78 1.38E−02 6 27 LGP52 0.87 2.26E−03 6 3LGP52 0.76 1.64E−02 6 25 LGP52 0.87 2.38E−03 6 5 LGP52 0.87 2.26E−03 623 LGP52 0.87 2.58E−03 6 61 LGP52 0.87 2.38E−03 6 24 LGP52 0.71 3.05E−026 26 LGP52 0.88 1.76E−03 6 21 LGP52 0.85 3.96E−03 6 57 Table 65.Provided are the correlations (R) between the expression levels yieldimproving genes and their homologues in various tissues [Expression sets(Exp)] and the phenotypic performance [yield, biomass, growth rateand/or vigor components (Correlation vector)] under abiotic stressconditions (salinity) or normal conditions across Sorghum accessions.Corr.—Correlation vector as described hereinabove (Table 63). P = pvalue.

Example 9 Production of Sorghum Transcriptome and High ThroughputCorrelation Analysis Using 60K Sorghum Oligonucleotide Micro-Array

In order to produce a high throughput correlation analysis between plantphenotype and gene expression level, the present inventors utilized asorghum oligonucleotide micro-array, produced by Agilent Technologies[chem. (dot) agilent (dot) com/Scripts/PDS (dot) asp?1Page=50879]. Thearray oligonucleotide represents about 60,000 sorghum genes andtranscripts. In order to define correlations between the levels of RNAexpression with vigor related parameters, various plant characteristicsof 10 different sorghum hybrids were analyzed. The correlation betweenthe RNA levels and the characterized parameters was analyzed usingPearson correlation test [davidmlane (dot) com/hyperstat/A34739 (dot)html].

Experimental Procedures

Correlation of Sorghum varieties across ecotypes grown in growthchambers under temperature of 30° C. or 14° C. at low light (100 μE) orhigh light (250 μE) conditions.

Analyzed Sorghum tissues—All 10 selected Sorghum hybrids were sampledper each condition. Leaf tissue growing under 30° C. and low light (100μE m⁻² sec⁻¹), 14° C. and low light (100 μE m⁻² sec⁻¹), 30° C. and highlight (250 μE m⁻² sec⁻¹), 14° C. and high light (250 μE m⁻² sec⁻¹) weresampled at vegetative stage of four-five leaves and RNA was extracted asdescribed above. Each micro-array expression information tissue type hasreceived a Set ID as summarized in Table 66 below.

TABLE 66 Sorghum transcriptome expression sets in field experimentsExpres- sion Description set Sorghum/leaf, under 14 Celsius degrees andhigh light (light on) 1 Sorghum/leaf, under 14 Celsius degrees and lowlight (light on) 2 Sorghum/leaf, under 30 Celsius degrees and high light(light on) 3 Sorghum/leaf, under 30 Celsius degrees and low light (lighton) 4 Table 66: Provided are the sorghum transcriptome expression sets.

The following parameters were collected by sampling 8-10 plants per plotor by measuring the parameter across all the plants within the plot(Table 67 below).

Relative Growth Rate of vegetative dry weight was performed usingFormula VII.

Leaves number—Plants were characterized for leaf number during growingperiod. In each measure, plants were measured for their leaf number bycounting all the leaves of selected plants per plot.

Shoot FW—shoot fresh weight (FW) per plant, measurement of allvegetative tissue above ground.

Shoot DW—shoot dry weight (DW) per plant, measurement of all vegetativetissue above ground after drying at 70° C. in oven for 48 hours.

The average for each of the measured parameters was calculated andvalues are summarized in Tables 68-71 below. Subsequent correlationanalysis was performed (Tables 72-75). Results were then integrated tothe database.

TABLE 67 Sorghum correlated parameters (vectors) Correlated parameterwith Correlation ID Leaves number 1 RGR (relative growth rate) 2 ShootDW (dry weight) (gr.) 3 Shoot FW (fresh weight) (gr.) 4 Table 67.Provided are the Sorghum correlated parameters (vectors).

TABLE 68 Measured parameters in Sorghum accessions under 14° C. and lowlight (100 μE m-² sec-¹) Ecotype/Treatment Line-1 Line-2 Line-3 Line-4Line-5 Line-6 Line-7 Line-8 Line-9 Line-10 1 3.00 3.00 2.75 2.75 2.633.00 3.50 2.75 2.43 2.00 2 0.032 −0.014 −0.022 0.024 −0.037 −0.045 0.083NA −0.050 −0.073 3 0.041 0.013 0.013 0.009 0.011 0.011 0.031 0.009 0.0090.009 4 0.55 0.30 0.33 0.28 0.36 0.36 0.58 0.22 0.18 0.30 Table 68:Provided are the values of each of the parameters (as described above)measured in Sorghum accessions (Seed ID) under 14° C. and low light (100μE m-² sec-¹).

TABLE 69 Measured parameters in Sorghum accessions under 30° C. and lowlight (100 μE m-² sec-¹) Ecotype/Treatment Line-1 Line-2 Line-3 Line-4Line-5 Line-6 Line-7 Line-8 Line-9 Line-10 1 5.27 5.00 4.75 4.00 4.004.00 5.25 4.50 3.75 4.00 2 0.099 0.098 0.090 0.122 0.108 0.084 0.1130.121 0.042 0.039 3 0.114 0.079 0.071 0.056 0.093 0.077 0.040 0.0550.036 0.050 4 1.35 1.05 0.88 0.95 1.29 1.13 0.71 0.79 0.67 0.82 Table69: Provided are the values of each of the parameters (as describedabove) measured in Sorghum accessions (Seed ID) under 30° C. and lowlight (100 μE m-² sec-¹).

TABLE 70 Measured parameters in Sorghum accessions under 30° C. and highlight (250 μE m-² sec-¹) Ecotype/Treatment Line-1 Line-2 Line-3 Line-4Line-5 Line-6 Line-7 Line-8 Line-9 Line-10 1 4.00 3.70 3.50 3.33 4.004.00 3.60 3.40 3.30 3.40 2 0.098 0.096 0.087 0.070 0.094 0.118 0.0970.099 0.106 0.121 3 0.076 0.050 0.047 0.036 0.065 0.085 0.049 0.0420.042 0.062 4 0.77 0.52 0.49 0.38 0.71 0.86 0.49 0.45 0.44 0.67 Table70: Provided are the values of each of the parameters (as describedabove) measured in Sorghum accessions (Seed ID) under 30° C. and highlight (250 μE m-² sec-¹).

TABLE 71 Measured parameters in Sorghum accessions under 14° C. and highlight (250 μE m-² sec-¹) Ecotype/Treatment Line-1 Line-2 Line-3 Line-4Line-5 Line-6 Line-7 Line-8 Line-9 Line-10 2 0.053 0.052 0.034 0.0400.056 0.061 0.049 0.056 0.068 0.063 3 0.037 0.026 0.021 0.023 0.0370.036 0.022 0.022 0.023 0.027 4 0.37 0.25 0.22 0.25 0.43 0.37 0.24 0.230.24 0.27 Table 71: Provided are the values of each of the parameters(as described above) measured in Sorghum accessions (Seed ID) under 14°C. and high light (250 μE m-² sec-¹).

TABLE 72 Correlation between the expression level of selected genes ofsome embodiments of the invention in various tissues and the phenotypicperformance Gene Name R P value Exp. set Corr. Set ID LGP52 0.758.85E−02 3 3 Table 72. Provided are the correlations (R) between theexpression levels of yield improving genes and their homologues intissues [Leaves or roots; Expression sets (Exp)] and the phenotypicperformance in various biomass, growth rate and/or vigor components[Correlation vector (corr.)] P = p value.

Example 10 Production of Sorghum Transcriptome and High ThroughputCorrelation Analysis with Yield and Drought Related Parameters Measuredin Fields Using 65K Sorghum Oligonucleotide Micro-Arrays

In order to produce a high throughput correlation analysis between plantphenotype and gene expression level, the present inventors utilized asorghum oligonucleotide micro-array, produced by Agilent Technologies[chem. (dot) agilent (dot) com/Scripts/PDS (dot) asp?1Page=50879]. Thearray oligonucleotide represents about 65,000 sorghum genes andtranscripts. In order to define correlations between the levels of RNAexpression with ABST, drought and yield components or vigor relatedparameters, various plant characteristics of 12 different sorghumhybrids were analyzed. Among them, 8 hybrids encompassing the observedvariance were selected for RNA expression analysis. The correlationbetween the RNA levels and the characterized parameters was analyzedusing Pearson correlation test [davidmlane (dot) com/hyperstat/A34739(dot) html].

Experimental Procedures

12 Sorghum varieties were grown in 6 repetitive plots, in field.Briefly, the growing protocol was as follows:

1. Regular growth conditions: sorghum plants were grown in the fieldusing commercial fertilization and irrigation protocols, which include452 m³ water per dunam (1000 square meters) per entire growth period andfertilization of 14 units nitrogen per dunam per entire growth period(normal conditions). The nitrogen can be obtained using URAN® 21%(Nitrogen Fertilizer Solution; PCS Sales, Northbrook, Ill., USA).

2. Drought conditions: sorghum seeds were sown in soil and grown undernormal condition until flowering stage (59 days from sowing), droughttreatment was imposed by irrigating plants with 50% water relative tothe normal treatment from this stage [309 m³ water per dunam (1000square meters) per the entire growth period)], with normal fertilization(i.e., 14 units nitrogen per dunam).

Analyzed Sorghum tissues—All 12 selected Sorghum hybrids were sampledper each treatment. Tissues [Flag leaf, upper stem, lower stem, flower,grain] representing different plant characteristics, from plants growingunder normal conditions and drought stress conditions were sampled andRNA was extracted as described above. Each micro-array expressioninformation tissue type has received a Set ID as summarized in Table 73below.

TABLE 73 Sorghum transcriptome expression sets in field experimentExpression Set Set ID Sorghum/flag leaf/Drought/flowering 1 Sorghum/flagleaf/Drought/grain filling 2 Table 73: Provided are the sorghumtranscriptome expression sets. Flag leaf = the leaf below the flower.

Sorghum Yield Components and Vigor Related Parameters Assessment

Plants were phenotyped using the parameters listed in Tables 74-75below. The following parameters were collected using digital imagingsystem:

Average Grain Area (cm²)—At the end of the growing period the grainswere separated from the Plant ‘Head’. A sample of ˜200 grains wasweighted, photographed and images were processed using the belowdescribed image processing system. The grain area was measured fromthose images and was divided by the number of grains.

Average Grain Length (cm)—At the end of the growing period the grainswere separated from the Plant ‘Head’. A sample of ˜200 grains wasweighted, photographed and images were processed using the belowdescribed image processing system. The sum of grain lengths (longestaxis) was measured from those images and was divided by the number ofgrains.

Average Grain Width (cm)—At the end of the growing period the grainswere separated from the Plant ‘Head’. A sample of ˜200 grains wasweighted, photographed and images were processed using the belowdescribed image processing system. The sum of grain width (longest axis)was measured from those images and was divided by the number of grains.

Average Grain Perimeter (cm)—At the end of the growing period the grainswere separated from the Plant ‘Head’. A sample of ˜200 grains wasweighted, photographed and images were processed using the belowdescribed image processing system. The sum of grain perimeter wasmeasured from those images and was divided by the number of grains.

Grain circularity—At the end of the growing period the grains wereseparated from the Plant ‘Head’. A sample of ˜200 grains was weighted,photographed and images were processed using the below described imageprocessing system. The circularity of the grains was calculated based onFormula XIX above.

Head Average Area (cm²)—At the end of the growing period 8 ‘Heads’ werephotographed and images were processed using the below described imageprocessing system. The ‘Head’ area was measured from those images andwas divided by the number of ‘Heads’.

Head Average Length (cm)—At the end of the growing period 8 ‘Heads’ werephotographed and images were processed using the below described imageprocessing system. The ‘Head’ length (longest axis) was measured fromthose images and was divided by the number of ‘Heads’.

Head Average Width (cm)—At the end of the growing period 8 ‘Heads’ werephotographed and images were processed using the below described imageprocessing system. The ‘Head’ width (longest axis) was measured fromthose images and was divided by the number of ‘Heads’.

An image processing system was used, which consists of a personaldesktop computer (Intel P4 3.0 GHz processor) and a public domainprogram—ImageJ 1.37, Java based image processing software, which wasdeveloped at the U.S. National Institutes of Health and is freelyavailable on the internet at rsbweb (dot) nih (dot) gov/. Images werecaptured in resolution of 10 Mega Pixels (3888×2592 pixels) and storedin a low compression JPEG (Joint Photographic Experts Group standard)format. Next, image processing output data for seed area and seed lengthwas saved to text files and analyzed using the JMP statistical analysissoftware (SAS institute).

Additional parameters were collected either by sampling 8 plants perplot or by measuring the parameter across all the plants within theplot.

Head dry weight at grain filling (gr.)—5 heads per plot were collectedat the grain filling stage (R2-R3) and weighted after oven dry (dryweight).

Head dry weights at harvest (gr.)—At the end of the growing period headswere collected (harvest stage), either from 8 plants per plot or fromthe rest of the plants in the plot. Heads were weighted after oven dry(dry weight), and average head weight per plant or per plot werecalculated.

Total Seed Yield (gr.)—At the end of the growing period heads werecollected (harvest stage). 8 heads were separately threshed and grainswere weighted. The average grain weight per plant was calculated bydividing the total grain weight by the number of plants.

1000 Seeds weight [gr]—weight of 1000 seeds per plot.

Grain number (num.)—was calculated by dividing seed yield by 1000 seedweight.

Plant height (cm.)—Plants were characterized for height during growingperiod at 6 time points (including at harvest). In each measure, plantswere measured for their height using a measuring tape. Height wasmeasured from ground level to top of the longest leaf.

SPAD—Chlorophyll content was determined using a Minolta SPAD 502chlorophyll meter and measurement was performed at early grain filling(SPAD_earlyGF) and late grain filling (SPAD_lateGF). SPAD meter readingswere done on fully developed leaf. Three measurements per leaf weretaken per plant.

Vegetative fresh and dry weight per plant (gr.)—At the end of thegrowing period all vegetative material (excluding roots) from plots werecollected and weighted before (fresh weight) and after (dry weight) ovendry. The biomass per plant was calculated by dividing total biomass bythe number of plants.

Relative water content (RWC, %)—at grain filling stage, leaves werecollected from 5 plants per plot. Measurements of relative water contentwas done as follows: fresh weight (FW) was recorded immediately afterleaf sampling; then leaves were soaked for 8 hours in distilled water atroom temperature in the dark, and the turgid weight (TW) was recorded.Total dry weight (DW) was recorded after drying the leaves at 60° C. toa constant weight. Relative water content (RWC) was calculated accordingto Formula I (above).

Specific Leaf Area (SLA)—at grain filling stage, leaves were collectedfrom 5 plants per plot. Leaves were scanned to obtain leaf area perplant, and then leaves were dried in an oven to obtain the leaves dryweight per plant. Specific leaf area was calculated by the leaf areadivided by leaf dry weight.

Stomatal conductance (F) (GF) (mmol m-2 s-1)—plants were evaluated fortheir stomata conductance using SC-1 Leaf Porometer (Decagon devices) atflowering (F) and at grain filling (GF) stages. Stomata conductancereadings were done on fully developed leaf, for 2 leaves and 2 plantsper plot.

Upper internode length (cm), width (cm) and volume (cm³)—Upperinternodes from at least 5 plants per plot were separated from the plantat flowering (F) and at harvest (H). Internodes were measured for theirlength (l) and width (d) using a ruler and a caliber. The internodevolume was calculated using Formula XX.

Upper internode fresh and dry density (F) and (H) (gr/cm³)—Theseparameters were measured at two time points during the course of theexperiment: at flowering (F) and at harvest (H). Upper internodes fromat least 5 plants per plot were separated from the plant and weighted(fresh and dry weight). To obtain stem density, stem weight (eitherfresh or dry) was divided by the stem volume (see above).

Lower internode length (cm), width (cm) and volume (cm³)—Lowerinternodes from at least 5 plants per plot were separated from the plantat flowering (F) and at harvest (H). Internodes were measured for theirlength (l) and width (d) using a ruler and a caliber. The internodevolume was calculated using Formula XX above.

Lower internode fresh and dry density (F) and (H) (gr/cm³)—Theseparameters were measured at two time points during the course of theexperiment: at flowering (F) and at harvest (H). Lower internodes fromat least 5 plants per plot were separated from the plant and weighted(fresh and dry weight). To obtain stem density, stem weight (eitherfresh or dry) was divided by the stem volume (see above).

Number of days to heading—Calculated as the number of days from sowingtill 50% of the plot arrives heading.

Number of days to maturity—Calculated as the number of days from sowingtill 50% of the plot arrives seed maturation.

Maintenance of performance under drought conditions—Represent ratio forthe specified parameter of Drought condition results divided by Normalconditions results (maintenance of phenotype under drought in comparisonto normal conditions).

Data parameters collected are summarized in Tables 74-75, herein below.

TABLE 74 Sorghum correlated parameters under drought conditions(vectors) Correlation Correlated parameter with ID % Canopy coverage(GF) under drought (%) 1 1000 grain weight under drought (gr) 2 GrainCircularity under drought (cm) 3 Grain Perimeter under drought (cm) 4Grain area under drought (cm²) 5 Grain length under drought (cm) 6 Grainwidth under drought (cm) 7 Grains number under drought (number) 8 Grainsweight per plant under drought (gr) 9 Head DW (GF) under drought (gr) 10Heads weight per plant under drought (gr) 11 Lower Stem dry density (H)under drought (cm³) 12 Lower Stem fresh density (F) under drought (cm³)13 Lower Stem width (F) under drought (cm) 14 Main Head Area underdrought (cm²) 15 Main Head Width under drought (cm) 16 Main Head lengthunder drought (cm) 17 Num Days to heading (field) under drought (days)18 Num days to maturity under drought (days) 19 Plant height underdrought (cm) 20 RWC_2 under drought (%) 21 SPAD_earlyGF under drought 22SPAD_lateGF under drought 23 Specific leaf area (GF) under drought(cm²/gr) 24 Stomatal conductance (F) under drought(mmol m−2 s−1) 25Stomatal conductance (GF) under drought (mmol m−2 s−1) 26 Upperinternode dry density (H) under drought (gr/cm³) 27 Upper internodefresh density (H) under drought (gr/cm³) 28 Upper internode length (H)under drought (cm) 29 Upper internode volume (H) under drought (cm³) 30Upper internode width (H) under drought (cm) 31 Vegetative DW per plantunder drought (gr) 32 Vegetative FW per plant under drought (gr) 33Table 74. Provided are the Sorghum correlated parameters (vectors).“gr.” = grams; “SPAD” = chlorophyll levels; “FW” = Plant Fresh weight;“DW” = Plant Dry weight; “GF”= grain filling growth stage; “F” =flowering stage; “H” = harvest stage.

TABLE 75 Sorghum correlated parameters for maintenance under droughtconditions (vectors) Correlated parameter with Correlation ID 1000grains weight D/N 1 Grain Perimeter D/N 2 Grain area D/N 3 Grain lengthD/N 4 Grain width D/N 5 Grains num (SP) D/N 6 Grains weight per plantD/N 7 Head DW (GF) D/N 8 Heads weight per plant (RP) D/N 9 Lower Stemwidth (F) D/N 10 Lower stem dry density (H) D/N 11 Lower stem freshdensity (F) D/N 12 Main Head Area D/N 13 Main Head Width D/N 14 MainHead length D/N 15 Plant height D/N 16 RWC_2 D/N 17 SPAD_2 D/N 18 SPAD_3D/N 19 Specific leaf area (GF) D/N 20 Stomatal conductance (F) D/N 21Stomatal conductance (GF) D/N 22 Upper Stem length (h) D/N 23 Upper Stemwidth (h) D/N 24 Upper stem dry density (H) D/N 25 Upper stem freshdensity (H) D/N 26 Upper stem volume (H) D/N 27 Vegetative DW per plantD/N 28 Vegetative FW per plant D/N 29 Table 75. Provided are the Sorghumcorrelated parameters (vectors). “gr.” = grams; “SPAD” = chlorophylllevels; “FW” = Plant Fresh weight; “DW” = Plant Dry weight; “Maintenanceunder drought” = calculated % of change under drought vs normal growthconditions. “GF” = grain filling growth stage; “F” = flowering stage;“H” = harvest stage.

Experimental Results

22 different sorghum hybrids were grown and characterized for differentparameters (Tables 74-75). The average for each of the measuredparameter was calculated using the JMP software (Tables 76-77) and asubsequent correlation analysis was performed (Tables 78-79). Resultswere then integrated to the database.

TABLE 76 Measured parameters in Sorghum accessions under droughtconditions Ecotype/Treatment Line-1 Line-2 Line-3 Line-4 Line-5 Line-6Line-7 Line-8 1 70.80 64.11 75.68 87.17 77.78 80.38 64.25 61.34 2 13.3017.88 20.24 17.95 14.64 20.83 15.43 19.80 3 0.88 0.90 0.90 0.89 0.880.89 0.89 0.87 4 1.20 1.22 1.28 1.30 1.27 1.36 1.24 1.28 5 0.10 0.110.12 0.12 0.11 0.13 0.11 0.11 6 0.39 0.40 0.41 0.42 0.42 0.45 0.40 0.417 0.33 0.34 0.36 0.36 0.34 0.37 0.34 0.35 8 17494.21 14526.20 15728.9613808.50 9838.55 12402.52 9979.86 5451.71 9 29.22 31.74 40.21 29.5218.23 34.43 19.10 13.67 10 19.29 33.15 27.31 50.38 37.04 11.72 9.3212.10 11 0.04 0.04 0.05 0.03 0.02 0.02 0.03 0.02 12 1.71 1.66 1.64 1.602.49 1.25 2.38 1.60 13 10.36 11.28 10.70 9.68 10.79 9.66 10.87 10.46 1414.90 13.32 14.53 17.27 18.35 13.96 17.19 16.63 15 114.58 94.24 104.2187.37 55.31 85.87 68.68 96.62 16 5.02 5.57 5.70 4.77 3.72 5.81 4.62 5.5317 31.12 22.16 24.36 24.76 19.93 19.41 19.90 24.79 18 63.00 56.00 59.6776.67 74.67 71.00 68.33 66.33 19 92.00 92.00 92.00 107.00 107.00 107.0092.00 92.00 20 80.92 93.43 104.15 105.63 69.04 133.54 47.82 83.24 2166.87 68.62 68.25 76.33 54.86 74.51 71.70 78.51 22 44.66 51.92 48.8437.60 38.19 43.35 47.58 46.97 23 30.93 43.69 37.80 32.49 34.14 25.8442.92 26.98 24 132.90 138.52 133.26 47.34 44.43 106.06 128. 67 143.32 25582.07 985.59 834.96 54.16 68.26 330.46 387.65 774.84 26 129.78 241.65322.92 127.17 276.22 217.19 81.21 561.18 27 1.65 1.62 1.63 1.76 1.921.66 1.55 1.43 28 5.18 5.39 5.40 5.53 8.60 3.60 4.61 5.72 29 48.60 48.7848.73 26.05 31.06 20.72 24.07 39.57 30 2865.28 2857.93 2955.99 1288.481128.61 1724.93 1507.76 2524.28 31 8.60 8.59 8.73 7.85 6.63 10.20 8.888.92 32 0.03 0.03 0.04 0.08 0.06 0.05 0.04 0.04 33 0.09 0.10 0.11 0.190.15 0.11 0.08 0.10 Table 76: Provided are the values of each of theparameters (as described above) measured in Sorghum accessions (Line)under drought conditions. Growth conditions are specified in theexperimental procedure section.

TABLE 77 Calculated parameters in Sorghum accessions under droughtconditions (maintenance of performance under drought vs normal growthconditions) Ecotype/Treatment Line-1 Line-2 Line-3 Line-4 Line-5 Line-6Line-7 Line-8 1 0.72 0.76 0.78 0.88 0.79 0.77 0.84 0.87 2 0.92 0.93 0.950.99 0.96 0.94 0.97 0.98 3 0.85 0.87 0.90 0.97 0.91 0.88 0.94 0.96 40.93 0.94 0.95 0.99 0.97 0.93 0.97 0.98 5 0.91 0.93 0.95 0.97 0.94 0.940.97 0.98 6 0.81 1.11 0.93 0.56 0.65 0.71 0.72 0.87 7 0.59 0.81 0.730.46 0.55 0.57 0.60 0.76 8 0.70 1.05 1.06 0.68 0.90 0.77 0.91 0.94 90.57 0.64 0.70 0.42 0.43 0.36 0.46 0.52 10 0.80 0.98 0.97 1.05 1.02 0.870.97 0.99 11 0.69 0.65 0.66 0.97 0.99 0.70 0.81 0.79 12 0.96 1.04 0.990.92 0.99 0.96 1.02 0.98 13 0.82 0.95 0.91 0.59 0.69 0.77 0.80 1.20 140.79 0.94 0.91 0.75 0.82 0.81 0.85 1.11 15 1.01 0.98 0.99 0.81 0.84 0.940.93 1.15 16 0.85 0.92 0.92 0.64 0.70 0.79 0.87 0.80 17 0.74 0.76 0.770.93 0.63 0.82 0.81 0.86 18 0.83 0.99 0.91 0.85 0.78 0.92 0.91 0.95 190.74 0.93 0.81 0.81 0.81 0.77 0.86 0.76 20 0.62 0.65 0.62 0.70 0.58 0.650.66 0.84 21 0.73 1.12 1.03 0.09 0.11 0.60 0.82 0.76 22 0.15 0.33 0.360.33 0.57 0.34 0.17 0.69 23 0.81 0.94 0.89 0.54 0.59 0.61 0.84 0.88 241.00 1.01 0.95 0.84 0.86 1.01 1.05 1.20 25 0.95 0.91 0.98 1.05 1.05 0.890.88 0.81 26 0.71 0.68 0.77 1.15 1.04 0.78 0.64 0.64 27 0.82 0.98 0.810.39 0.46 0.62 0.94 1.16 28 0.74 0.71 0.69 0.77 0.82 0.77 0.85 0.78 290.60 0.69 0.59 0.80 0.68 0.73 0.66 0.69 Table 77: Provided are thevalues of each of the parameters (as described above) measured insorghum accessions (line) for maintenance of performance under drought(calculated as % of change under drought vs normal growth conditions).Growth conditions are specified in the experimental procedure section.

TABLE 78 Correlation between the expression level of selected genes ofsome embodiments of the invention in various tissues and the phenotypicperformance under drought stress conditions across Sorghum accessionsGene Exp. Corr. Gene Exp. Corr. Name R P value set Set ID Name R P valueset Set ID LGP102 0.97 4.03E−04 1 21 LGP102 0.74 5.51E−02 1 20 LGP1020.76 4.88E−02 1 6 LGP102 0.78 4.05E−02 1 5 LGP102 0.82 2.50E−02 1 4LGP102 0.73 6.51E−02 1 19 LGP102 0.76 4.66E−02 1 7 LGP102 0.78 3.91E−022 14 LGP102 0.78 3.72E−02 2 32 LGP102 0.94 1.59E−03 2 18 LGP52 0.851.54E−02 1 3 LGP52 0.76 4.58E−02 1 23 LGP52 0.85 1.65E−02 2 3 LGP52 0.717.40E−02 2 12 LGP52 0.79 3.46E−02 2 9 LGP52 0.80 3.18E−02 2 23 Table 78.Correlations (R) between the genes expression levels in various tissuesand the phenotypic performance. “Corr. ID”—correlation set ID accordingto the correlated parameters Table above. “Exp. Set”—Expression set. “R”= Pearson correlation coefficient; “P” = p value.

TABLE 79 Correlation between the expression level of selected genes ofsome embodiments of the invention in various tissues and the phenotypicperformance of maintenance of performance under drought across Sorghumaccessions Gene Exp. Corr. Gene Exp. Corr. Name R P value set Set IDName R P value set Set ID LGP102 0.71 7.45E-02 1 1 LGP102 0.81 2.78E-021 22 LGP102 0.87 1.12E-02 1 20 LGP102 0.73 6.26E-02 1 17 LGP102 0.755.39E-02 1 5 LGP102 0.73 6.30E-02 2 1 LGP102 0.72 6.70E-02 2 28 LGP1020.75 5.30E-02 2 2 LGP102 0.71 7.28E-02 2 3 LGP102 0.88 9.67E-03 2 11LGP102 0.79 3.27E-02 2 17 LGP52 0.72 6.64E-02 1 16 Table 79.Correlations (R) between the genes expression levels in various tissuesand the phenotypic performance. “Corr. ID”—correlation set ID accordingto the correlated parameters Table above. “Exp. Set”—Expression set. “R”= Pearson correlation coefficient; “P” = p value.

Example 11 Production of Maize Transcriptome and High ThroughputCorrelation Analysis Using 60K Maize Oligonucleotide Micro-Array

To produce a high throughput correlation analysis, the present inventorsutilized a Maize oligonucleotide micro-array, produced by AgilentTechnologies [chem. (dot) agilent (dot) com/Scripts/PDS (dot)asp?1Page=50879]. The array oligonucleotide represents about 60K Maizegenes and transcripts designed based on data from Public databases(Example 1). To define correlations between the levels of RNA expressionand yield, biomass components or vigor related parameters, various plantcharacteristics of 12 different Maize hybrids were analyzed. Among them,10 hybrids encompassing the observed variance were selected for RNAexpression analysis. The correlation between the RNA levels and thecharacterized parameters was analyzed using Pearson correlation test[davidmlane (dot) com/hyperstat/A34739 (dot) html].

Experimental Procedures

All 10 selected maize hybrids were sampled in three time points(TP2=V2-V3 (when two to three collar leaf are visible, rapid growthphase and kernel row determination begins), TP5=R1-R2 (silking-blister),TP6=R3-R4 (milk-dough). Four types of plant tissues [Ear, flag leafindicated in Table as leaf, grain distal part, and internode] weresampled and RNA was extracted as described in “GENERAL EXPERIMENTAL ANDBIOINFORMATICS METHODS”. For convenience, each micro-array expressioninformation tissue type has received a Set ID as summarized in Table 80below.

TABLE 80 Tissues used for Maize transcriptome expression sets SetExpression Set ID Ear under normal conditions at reproductive stage:R1-R2 1 Ear under normal conditions at reproductive stage: R3-R4 2Internode under normal conditions at vegetative stage: Vegetative 3 V2-3Internode under normal conditions at reproductive stage: R1-R2 4Internode under normal conditions at reproductive stage: R3-R4 5 Leafunder normal conditions at vegetative stage: Vegetative V2-3 6 Leafunder normal conditions at reproductive stage: R1-R2 7 Grain distalunder normal conditions at reproductive stage: R1-R2 8 Table 80:Provided are the identification (ID) number of each of the Maizeexpression sets

The following parameters were collected:

Grain Area (cm²)—At the end of the growing period the grains wereseparated from the ear. A sample of ˜200 grains was weighted,photographed and images were processed using the below described imageprocessing system. The grain area was measured from those images and wasdivided by the number of grains.

Grain Length and Grain width (cm)—At the end of the growing period thegrains were separated from the ear. A sample of ˜200 grains wasweighted, photographed and images were processed using the belowdescribed image processing system. The sum of grain lengths/or width(longest axis) was measured from those images and was divided by thenumber of grains.

Ear Area (cm²)—At the end of the growing period 6 ears were,photographed and images were processed using the below described imageprocessing system. The Ear area was measured from those images and wasdivided by the number of Ears.

Ear Length and Ear Width (cm)—At the end of the growing period 6 earswere photographed and images were processed using the below describedimage processing system. The Ear length and width (longest axis) wasmeasured from those images and was divided by the number of ears.

Filled per Whole Ear—it was calculated as the length of the ear withgrains out of the total ear.

Percent Filled Ear—At the end of the growing period 6 ears werephotographed and images were processed using the below described imageprocessing system. The percent filled Ear grain was the ear with grainsout of the total ear and was measured from those images and was dividedby the number of Ears.

The image processing system was used, which consists of a personaldesktop computer (Intel P4 3.0 GHz processor) and a public domainprogram—ImageJ 1.37, Java based image processing software, which wasdeveloped at the U.S. National Institutes of Health and is freelyavailable on the internet at rsbweb (dot) nih (dot) gov/. Images werecaptured in resolution of 10 Mega Pixels (3888×2592 pixels) and storedin a low compression JPEG (Joint Photographic Experts Group standard)format. Next, image processing output data for seed area and seed lengthwas saved to text files and analyzed using the JMP statistical analysissoftware (SAS institute).

Additional parameters were collected either by sampling 6 plants perplot or by measuring the parameter across all the plants within theplot.

Normalized Grain Weight per plant (gr.), measurement of yieldparameter—At the end of the experiment all ears from plots within blocksA-C were collected. Six ears were separately threshed and grains wereweighted, all additional ears were threshed together and weighted aswell. The grain weight was normalized using the relative humidity to be0%. The normalized average grain weight per ear was calculated bydividing the total normalized grain weight by the total number of earsper plot (based on plot). In case of 6 ears, the total grains weight of6 ears was divided by 6.

Ear fresh weight (FW) (gr.)—At the end of the experiment (when ears wereharvested) total and 6 selected ears per plots within blocks A-C werecollected separately. The plants' ears (total and 6) were weighted (gr.)separately and the average ear per plant was calculated for total (EarFW per plot) and for 6 (Ear FW per plant).

Plant height and Ear height—Plants were characterized for height atharvesting. In each measure, 6 plants were measured for their heightusing a measuring tape. Height was measured from ground level to top ofthe plant below the tassel. Ear height was measured from the groundlevel to the place were the main ear is located

Leaf number per plant—Plants were characterized for leaf number duringgrowing period at 5 time points. In each measure, plants were measuredfor their leaf number by counting all the leaves of 3 selected plantsper plot.

Relative Growth Rate was calculated using regression coefficient of leafnumber change a long time course.

SPAD—Chlorophyll content was determined using a Minolta SPAD 502chlorophyll meter and measurement was performed 64 days post sowing.SPAD meter readings were done on young fully developed leaf. Threemeasurements per leaf were taken per plot. Data were taken after 46 and54 days after sowing (DPS). Dry weight=total weight of the vegetativeportion above ground (excluding roots) after drying at 70° C. in ovenfor 48 hours.

Dry weight per plant—At the end of the experiment when all vegetativematerial from plots within blocks A-C were collected, weight and dividedby the number of plants.

Ear diameter [cm]—The diameter of the ear at the mid of the ear wasmeasured using a ruler.

Cob diameter [cm]—The diameter of the cob without grains was measuredusing a ruler.

Kernel Row Number per Ear—The number of rows in each ear was counted.The average of 6 ears per plot was calculated.

Leaf area index [LAI]=total leaf area of all plants in a plot.Measurement was performed using a Leaf area-meter.

Yield/LAI [kg]—is the ratio between total grain yields and total leafarea index.

TABLE 81 Maize correlated parameters (vectors) Correlated parameter withCorrelation ID Cob Diameter (mm) 1 DW per Plant based on 6 (gr.) 2 EarArea (cm²) 3 Ear FW per Plant based on 6 (gr.) 4 Ear Height (cm) 5 EarLength (cm) 6 Ear Width (cm) 7 Ears FW per plant based on all (gr.) 8Filled per Whole Ear 9 Grain Area (cm²) 10 Grain Length (cm) 11 GrainWidth (cm) 12 Growth Rate Leaf Number 13 Kernel Row Number per Ear 14Leaf Number per Plant 15 Normalized Grain Weight per Plant based on all(gr.) 16 Normalized Grain Weight per plant based on 6 (gr.) 17 PercentFilled Ear 18 Plant Height per Plot (cm) 19 SPAD R1 20 SPAD R2 21 Table81.

Experimental Results

Twelve maize varieties were grown and characterized for parameters, asdescribed above. The average for each parameter was calculated using theJMP software, and values are summarized in Tables 82-83 below.Subsequent correlation between the various transcriptome sets for all orsub sets of lines was done by the bioinformatic unit and results wereintegrated into the database (Table 84 below).

TABLE 82 Measured parameters in Maize Hybrid Ecotype/ Treatment Line-1Line-2 Line-3 Line-4 Line-5 Line-6 1 28.96 25.08 28.05 25.73 28.72 25.782 657.50 491.67 641.11 580.56 655.56 569.44 3 85.06 85.84 90.51 95.9591.62 72.41 4 245.83 208.33 262.22 263.89 272.22 177.78 5 135.17 122.33131.97 114.00 135.28 94.28 6 19.69 19.05 20.52 21.34 20.92 18.23 7 5.585.15 5.67 5.53 5.73 5.23 8 278.19 217.50 288.28 247.88 280.11 175.84 90.916 0.922 0.927 0.917 0.908 0.950 10 0.75 0.71 0.75 0.77 0.81 0.71 111.17 1.09 1.18 1.20 1.23 1.12 12 0.81 0.81 0.80 0.80 0.82 0.80 13 0.280.22 0.28 0.27 0.31 0.24 14 16.17 14.67 16.20 15.89 16.17 15.17 15 12.0011.11 11.69 11.78 11.94 12.33 16 153.90 135.88 152.50 159.16 140.46117.14 17 140.68 139.54 153.67 176.98 156.61 119.67 18 80.62 86.76 82.1492.71 80.38 82.76 19 278.08 260.50 275.13 238.50 286.94 224.83 20 51.6756.41 53.55 55.21 55.30 59.35 21 54.28 57.18 56.01 59.68 54.77 59.14

TABLE 83 Measured parameters in Maize Hybrid additional parametersEcotype/ Treatment Line-7 Line-8 Line-9 Line-10 Line-11 Line-12 1 26.4325.19 26.67 2 511.11 544.44 574.17 522.22 3 74.03 76.53 55.20 95.36 4188.89 197.22 141.11 261.11 5 120.94 107.72 60.44 112.50 6 19.02 18.5716.69 21.70 7 5.22 5.33 4.12 5.58 8 192.47 204.70 142.72 264.24 9 0.870.94 0.80 0.96 10 0.71 0.75 0.50 0.76 11 1.14 1.13 0.92 1.18 12 0.790.84 0.67 0.81 13 0.24 0.27 0.19 0.30 14 16.00 14.83 14.27 15.39 1512.44 12.22 9.28 12.56 16 123.24 131.27 40.84 170.66 17 119.69 133.5154.32 173.23 18 73.25 81.06 81.06 91.60 19 264.44 251.61 163.78 278.4420 58.48 55.88 52.98 53.86 59.75 49.99 21 57.99 60.36 54.77 51.39 61.1453.34

TABLE 84 Correlation between the expression level of selected genes ofsome embodiments of the invention in various tissues and the phenotypicperformance under normal conditions across maize varieties Gene Exp.Corr. Gene Exp. Corr. Name R P value set Set ID Name R P value set SetID LGP25 0.85 1.58E−02 1 2 LGP27 0.93 2.27E−03 4 14 LGP25 0.71 1.17E−014 1 LGP25 0.94 4.53E−03 1 1 LGP27 0.72 6.78E−02 1 5 LGP27 0.79 6.16E−022 12 LGP27 0.74 5.74E−02 4 11 LGP27 0.73 6.00E−02 4 5 LGP27 0.755.15E−02 4 7 LGP27 0.75 5.32E−02 4 8 LGP27 0.73 6.45E−02 4 4 LGP27 0.726.91E−02 1 19 LGP72 0.75 8.34E−02 2 15 LGP72 0.74 9.47E−02 2 12 LGP720.76 4.63E−02 4 3 LGP72 0.75 5.29E−02 4 16 LGP72 0.89 6.57E−03 4 14LGP72 0.75 5.04E−02 4 15 LGP72 0.84 1.70E−02 4 13 LGP72 0.76 4.74E−02 411 LGP72 0.85 1.63E−02 4 6 LGP72 0.73 6.09E−02 4 9 LGP72 0.78 3.83E−02 47 LGP72 0.87 1.03E−02 4 8 LGP72 0.86 1.33E−02 4 4 LGP72 0.74 5.92E−02 417 LGP72 0.75 5.21E−02 7 3 LGP72 0.71 7.50E−02 7 14 LGP72 0.74 5.95E−027 5 LGP72 0.73 6.43E−02 7 17 LGP73 0.77 7.45E−02 1 1 LGP73 0.86 2.66E−033 18 LGP73 0.88 2.06E−02 4 1 LGP73 0.75 5.43E−02 4 2 LGP74 0.82 1.27E−025 12 LGP74 0.78 3.70E−02 4 2 LGP75 0.90 5.34E−03 1 16 LGP75 0.764.78E−02 1 14 LGP75 0.85 1.52E−02 1 15 LGP75 0.81 2.76E−02 1 13 LGP750.89 6.95E−03 1 11 LGP75 0.80 3.10E−02 1 6 LGP75 0.89 6.96E−03 1 9 LGP750.87 1.02E−02 1 10 LGP75 0.87 1.19E−02 1 19 LGP75 0.81 2.86E−02 1 5LGP75 0.92 3.16E−03 1 7 LGP75 0.79 3.34E−02 1 8 LGP75 0.78 3.95E−02 1 12LGP75 0.79 3.37E−02 1 4 LGP75 0.86 1.32E−02 1 17 LGP75 0.77 2.58E−02 812 LGP75 0.72 1.03E−01 2 18 LGP80 0.76 2.82E−02 5 14 LGP75 0.74 2.16E−023 16 LGP75 0.71 3.26E−02 3 17 LGP75 0.87 1.07E−02 4 2 LGP75 0.831.94E−02 1 3 LGP75 0.80 1.81E−02 5 3 LGP75 0.93 6.85E−03 4 1 LGP75 0.823.48E−03 6 3 LGP75 0.78 7.94E−03 6 16 LGP75 0.82 3.49E−03 6 14 LGP750.79 6.20E−03 6 11 LGP75 0.81 4.64E−03 6 6 LGP75 0.71 2.18E−02 6 10LGP75 0.73 1.61E−02 6 5 LGP75 0.80 5.68E−03 6 7 LGP75 0.84 2.14E−03 6 8LGP75 0.87 1.07E−03 6 4 LGP75 0.80 5.74E−03 6 17 LGP75 0.74 2.14E−02 3 3LGP80 0.83 4.31E−02 4 1 LGP82 0.86 2.69E−02 1 1 LGP82 0.71 7.33E−02 1 8LGP82 0.81 8.59E−03 3 5 LGP82 0.72 2.97E−02 3 8 LGP82 0.86 2.88E−02 2 12LGP86 0.72 6.82E−02 1 3 LGP86 0.79 3.40E−02 1 16 LGP86 0.90 6.16E−03 114 LGP86 0.73 5.99E−02 1 15 LGP86 0.77 4.11E−02 1 13 LGP86 0.89 7.89E−031 11 LGP86 0.74 5.87E−02 1 9 LGP86 0.86 1.39E−02 1 10 LGP86 0.764.97E−02 1 19 LGP86 0.82 2.24E−02 1 5 LGP86 0.91 4.28E−03 1 7 LGP86 0.803.22E−02 1 8 LGP86 0.74 5.82E−02 1 12 LGP86 0.76 4.68E−02 1 4 LGP86 0.764.60E−02 1 17 LGP86 0.76 2.76E−02 8 18 LGP86 0.72 2.88E−02 3 16 LGP860.72 2.81E−02 3 19 LGP86 0.81 7.92E−03 3 5 LGP86 0.76 1.86E−02 3 7 LGP860.78 1.32E−02 3 8 LGP87 0.71 2.19E−02 6 20 LGP86 0.87 1.17E−02 4 16LGP86 0.90 6.32E−03 4 14 LGP86 0.71 7.43E−02 4 13 LGP86 0.86 1.33E−02 411 LGP86 0.84 1.74E−02 4 6 LGP86 0.80 2.90E−02 4 10 LGP86 0.82 2.41E−024 19 LGP86 0.92 3.17E−03 4 5 LGP86 0.88 8.16E−03 4 7 LGP86 0.94 1.93E−034 8 LGP86 0.92 3.57E−03 4 4 LGP86 0.86 1.20E−02 4 17 LGP86 0.72 4.27E−025 9 LGP86 0.90 5.39E−03 4 3 LGP86 0.98 1.25E−04 7 3 LGP86 0.90 5.89E−037 16 LGP86 0.82 2.51E−02 7 11 LGP86 0.92 3.20E−03 7 6 LGP86 0.774.11E−02 7 10 LGP86 0.78 3.66E−02 7 18 LGP86 0.79 3.42E−02 7 19 LGP860.85 1.47E−02 7 5 LGP86 0.81 2.89E−02 7 7 LGP86 0.87 1.03E−02 7 8 LGP860.93 2.46E−03 7 4 LGP86 0.93 2.24E−03 7 17 LGP88 0.79 6.15E−02 2 6 LGP890.77 4.11E−02 4 14 LGP88 0.77 7.40E−02 4 1 LGP88 0.77 7.59E−02 1 1 LGP890.75 5.29E−02 1 2 LGP89 0.71 2.07E−02 6 3 LGP89 0.73 1.02E−01 2 12 LGP900.86 2.80E−02 7 1 LGP89 0.77 4.31E−02 4 6 LGP89 0.71 7.64E−02 4 18 LGP890.77 4.22E−02 4 4 LGP89 0.71 1.15E−01 1 1 LGP89 0.71 2.05E−02 6 6 LGP890.71 2.25E−02 6 7 LGP89 0.80 5.58E−03 6 8 LGP89 0.77 9.49E−03 6 4 LGP900.74 5.66E−02 1 3 LGP90 0.77 4.10E−02 1 16 LGP90 0.72 6.54E−02 1 9 LGP900.78 3.89E−02 1 10 LGP90 0.83 2.19E−02 1 19 LGP90 0.91 4.05E−03 1 5LGP90 0.72 6.56E−02 1 7 LGP90 0.85 1.51E−02 1 12 LGP90 0.74 5.61E−02 117 LGP90 0.81 4.96E−02 2 14 LGP91 0.74 5.75E−02 1 3 LGP91 0.73 1.62E−026 20 LGP91 0.72 1.05E−01 2 2 LGP92 0.77 4.39E−02 4 2 LGP91 0.74 3.59E−025 18 LGP91 0.81 2.77E−02 7 3 LGP91 0.74 5.89E−02 7 16 LGP91 0.736.14E−02 7 19 LGP91 0.83 2.14E−02 7 5 LGP91 0.76 4.71E−02 7 17 LGP920.92 8.68E−03 2 14 LGP92 0.73 1.01E−01 2 5 LGP92 0.82 1.34E−02 8 1 LGP920.83 1.07E−02 8 2 LGP94 0.84 3.67E−02 1 1 LGP94 0.71 1.12E−01 2 12 LGP940.80 3.14E−02 4 15 LGP94 0.82 2.34E−02 4 9 LGP94 0.74 5.96E−02 4 19LGP94 0.80 3.05E−02 4 12 LGP95 0.74 1.48E−02 6 3 LGP95 0.71 2.05E−02 610 LGP95 0.75 1.24E−02 6 4 LGP95 0.71 2.02E−02 6 17 Table 84. Providedare the correlations (R) between the expression levels yield improvinggenes and their homologs in various tissues [Expression (Exp) sets] andthe phenotypic performance [yield, biomass, growth rate and/or vigorcomponents (Correlation vector (Corr.))] under normal conditions acrossmaize varieties. P = p value.

Example 12 Production of Maize Transcriptome and High ThroughputCorrelation Analysis with Yield, NUE, and ABST Related ParametersMeasured in Semi-Hydroponics Conditions Using 60K Maize OligonucleotideMicro-Arrays

Maize vigor related parameters under low nitrogen, 100 mM NaCl, lowtemperature (10±2° C.) and normal growth conditions—Twelve Maize hybridswere grown in 5 repetitive plots, each containing 7 plants, at a nethouse under semi-hydroponics conditions. Briefly, the growing protocolwas as follows: Maize seeds were sown in trays filled with a mix ofvermiculite and peat in a 1:1 ratio. Following germination, the trayswere transferred to the high salinity solution (100 mM NaCl in additionto the Full Hoagland solution), low temperature (“cold conditions” of10±2° C. in the presence of Full Hoagland solution), low nitrogensolution (the amount of total nitrogen was reduced in 90% from the fullHoagland solution (i.e., to a final concentration of 10% from fullHoagland solution, final amount of 1.6 mM N) or at Normal growthsolution (Full Hoagland containing 16 mM N solution, at 28±2° C.).Plants were grown at 28±2° C.

Full Hoagland solution consists of: KNO₃—0.808 grams/liter, MgSO₄—0.12grams/liter, KH₂PO₄—0.136 grams/liter and 0.01% (volume/volume) of‘Super coratin’ micro elements (Iron-EDDHA[ethylenediamine-N,N′-bis(2-hydroxyphenyl acetic acid)]—40.5grams/liter; Mn—20.2 grams/liter; Zn 10.1 grams/liter; Co 1.5grams/liter; and Mo 1.1 grams/liter), solution's pH should be 6.5-6.8].

Analyzed Maize tissues—Twelve selected Maize hybrids were sampled pereach treatment. Two tissues [leaves and root tip] growing at 100 mMNaCl, low temperature (10±2° C.), low Nitrogen (1.6 mM N) or underNormal conditions were sampled at the vegetative stage (V4-5) and RNAwas extracted as described above. Each micro-array expressioninformation tissue type has received a Set ID as summarized in Table85-88 below.

TABLE 85 Maize transcriptome expression sets under semi hydroponicsconditions Expression set Set ID leaf at vegetative stage (V4-V5) underNormal conditions 1 root tip at vegetative stage (V4-V5) under Normalconditions 2 Table 85: Provided are the Maize transcriptome expressionsets at normal conditions.

TABLE 86 Maize transcriptome expression sets under semi hydroponicsconditions Expression set Set ID leaf at vegetative stage (V4-V5) undercold conditions 1 root tip at vegetative stage (V4-V5) under coldconditions 2 Table 86: Provided are the Maize transcriptome expressionsets at cold conditions.

TABLE 87 Maize transcriptome expression sets under semi hydroponicsconditions Expression set Set ID leaf at vegetative stage (V4-V5) underlow N conditions 1 (1.6 mM N) root tip at vegetative stage (V4-V5) underlow N conditions 2 (1.6 mM N) Table 87: Provided are the Maizetranscriptome expression sets at low nitrogen conditions 1.6 MmNitrogen.

TABLE 88 Maize transcriptome expression sets under semi hydroponicsconditions Expression set Set ID leaf at vegetative stage (V4-V5) undersalinity conditions 1 (NaCl 100 mM) root tip at vegetative stage (V4-V5)under salinity conditions 2 (NaCl 100 mM) Table 88: Provided are theMaize transcriptome expression sets at 100 mM NaCl.

The following parameters were collected:

Leaves DW—leaves dry weight per plant (average of five plants).

Plant Height growth—was calculated as regression coefficient of plantheight [cm] along time course (average of five plants).

Root DW—root dry weight per plant, all vegetative tissue above ground(average of four plants).

Root length—the length of the root was measured at V4 developmentalstage.

Shoot DW—shoot dry weight per plant, all vegetative tissue above ground(average of four plants) after drying at 70° C. in oven for 48 hours.

Shoot FW—shoot fresh weight per plant, all vegetative tissue aboveground (average of four plants).

SPAD—Chlorophyll content was determined using a Minolta SPAD 502chlorophyll meter and measurement was performed 30 days post sowing.SPAD meter readings were done on young fully developed leaf. Threemeasurements per leaf were taken per plot.

Experimental Results

12 different Maize hybrids were grown and characterized at thevegetative stage (V4-5) for different parameters. The correlatedparameters are described in Table 89 below. The average for each of themeasured parameter was calculated using the JMP software and values aresummarized in Tables 90-97 below. Subsequent correlation analysis wasperformed (Table 98-101). Results were then integrated to the database.

TABLE 89 Maize correlated parameters (vectors) Correlated parameter withCorrelation ID Leaves DW [gr] 1 Plant height growth [cm/day] 2 Root DW[gr] 3 Root length [cm] 4 SPAD 5 Shoot DW [gr] 6 Shoot FW [gr] 7 Table89: Provided are the Maize correlated parameters.

TABLE 90 Maize accessions, measured parameters under low nitrogen growthconditions Ecotype/ Treatment Line-1 Line-2 Line-3 Line-4 Line-5 Line-61 0.57 0.45 0.46 0.48 0.36 0.51 2 0.75 0.81 0.88 0.69 0.83 0.84 3 0.380.35 0.25 0.36 0.31 0.30 4 44.50 45.63 44.25 43.59 40.67 42.03 5 21.4321.24 22.23 24.56 22.75 26.47 6 2.56 1.96 2.01 1.94 1.94 2.52 7 23.2720.58 19.26 20.02 17.98 22.06 Table 90: Provided are the values of eachof the parameters (as described above) measured in Maize accessions(Seed ID) under low nitrogen conditions. Growth conditions are specifiedin the experimental procedure section.

TABLE 91 Maize accessions, measured parameters under low nitrogen growthconditions Ecotype/ Treatment Line-7 Line-8 Line-9 Line-10 Line-11Line-12 1 0.53 0.58 0.55 0.51 0.56 0.39 2 0.78 0.92 0.89 0.85 0.80 0.643 0.29 0.31 0.29 0.32 0.43 0.17 4 42.65 45.06 45.31 42.17 41.03 37.65 522.08 25.09 23.73 25.68 25.02 19.51 6 2.03 2.37 2.09 2.17 2.62 1.53 721.28 22.13 20.29 19.94 22.50 15.93 Table 91: Provided are the values ofeach of the parameters (as described above) measured in Maize accessions(Seed ID) under low nitrogen conditions. Growth conditions are specifiedin the experimental procedure section.

TABLE 92 Maize accessions, measured parameters under 100 mM NaCl growthconditions Ecotype/ Treatment Line-1 Line-2 Line-3 Line-4 Line-5 Line-61 0.41 0.50 0.43 0.48 0.43 0.56 2 0.46 0.40 0.45 0.32 0.32 0.31 3 0.050.05 0.03 0.07 0.05 0.03 4 10.88 11.28 11.82 10.08 8.46 10.56 5 36.5539.92 37.82 41.33 40.82 44.40 6 2.43 2.19 2.25 2.26 1.54 1.94 7 19.5820.78 18.45 19.35 15.65 16.09 Table 92: Provided are the values of eachof the parameters (as described above) measured in Maize accessions(Seed ID) under 100 mM NaCl growth conditions. Growth conditions arespecified in the experimental procedure section.

TABLE 93 Maize accessions, measured parameters under 100 mM NaCl growthconditions Ecotype/ Treatment Line-7 Line-8 Line-9 Line-10 Line-11Line-12 1 0.33 0.51 0.47 0.98 0.48 0.15 2 0.29 0.36 0.37 0.35 0.31 0.273 0.10 0.06 0.02 0.04 0.05 0.01 4 10.14 11.83 10.55 11.18 10.09 8.90 537.92 43.22 39.83 38.20 38.14 37.84 6 1.78 1.90 1.89 2.20 1.86 0.97 712.46 16.92 16.75 17.64 15.90 9.40 Table 93: Provided are the values ofeach of the parameters (as described above) measured in Maize accessions(Seed ID) under 100 mM NaCl growth conditions. Growth conditions arespecified in the experimental procedure section.

TABLE 94 Maize accessions, measured parameters under cold growthconditions Ecotype/ Treatment Line-1 Line-2 Line-3 Line-4 Line-5 Line-61 1.19 1.17 1.02 1.18 1.04 1.23 2 2.15 1.93 2.12 1.80 2.32 2.15 3 0.050.07 0.10 0.08 0.07 0.07 5 28.88 29.11 27.08 32.38 32.68 32.89 6 5.744.86 3.98 4.22 4.63 4.93 7 73.79 55.46 53.26 54.92 58.95 62.36 Table 94:Provided are the values of each of the parameters (as described above)measured in Maize accessions (Seed ID) under cold growth conditions.Growth conditions are specified in the experimental procedure section.

TABLE 95 Maize accessions, measured parameters under cold growthconditions Ecotype/ Treatment Line-7 Line-8 Line-9 Line-10 Line-11Line-12 1 1.13 0.98 0.88 1.28 1.10 0.60 2 2.49 2.01 1.95 2.03 1.85 1.213 0.14 0.07 0.07 0.02 0.05 0.06 5 31.58 33.01 28.65 31.43 30.64 30.71 64.82 4.03 3.57 3.99 4.64 1.89 7 63.65 54.90 48.25 52.83 55.08 29.61Table 95: Provided are the values of each of the parameters (asdescribed above) measured in Maize accessions (Seed ID) under coldgrowth conditions. Growth conditions are specified in the experimentalprocedure section.

TABLE 96 Maize accessions, measured parameters under regular growthconditions Ecotype/ Treatment Line-1 Line-2 Line-3 Line-4 Line-5 Line-61 1.16 1.10 0.92 1.01 0.93 0.91 2 1.99 1.92 1.93 1.93 2.15 1.95 3 0.140.11 0.23 0.16 0.08 0.05 4 20.15 15.89 18.59 18.72 16.38 14.93 5 34.5035.77 34.70 34.42 35.26 37.52 6 5.27 4.67 3.88 5.08 4.10 4.46 7 79.0062.85 59.73 63.92 60.06 64.67 Table 96: Provided are the values of eachof the parameters (as described above) measured in Maize accessions(Seed ID) under regular growth conditions. Growth conditions arespecified in the experimental procedure section.

TABLE 97 Maize accessions, measured parameters under regular growthconditions Ecotype/ Treatment Line-7 Line-8 Line-9 Line-10 Line-11Line-12 1 1.11 1.01 1.01 1.02 1.23 0.44 2 2.23 1.94 1.97 2.05 1.74 1.263 0.17 0.10 0.07 0.10 0.14 0.03 4 17.48 15.74 15.71 17.58 16.13 17.43 536.50 36.07 33.74 34.34 35.74 29.04 6 4.68 4.59 4.08 4.61 5.42 2.02 768.10 65.81 58.31 61.87 70.04 35.96 Table 97: Provided are the values ofeach of the parameters (as described above) measured in Maize accessions(Seed ID) under regular growth conditions. Growth conditions arespecified in the experimental procedure section.

TABLE 98 Correlation between the expression level of selected genes ofsome embodiments of the invention in various tissues and the phenotypicperformance under normal conditions across Maize accessions Gene Exp.Corr. Gene Exp. Corr. Name R P value set Set ID Name R P value set SetID LGP25 0.74 2.15E−02 2 7 LGP25 0.75 1.99E−02 2 6 LGP72 0.71 2.02E−02 13 LGP72 0.70 2.29E−02 1 6 LGP74 0.83 2.88E−03 1 4 LGP75 0.71 2.02E−02 17 LGP75 0.77 9.15E−03 1 2 LGP75 0.71 2.07E−02 1 1 LGP75 0.73 1.61E−02 14 LGP92 0.80 9.13E−03 2 7 LGP92 0.72 2.94E−02 2 6 Table 98. Provided arethe correlations (R) between the expression levels of yield improvinggenes and their homologues in tissues [Leaves or roots; Expression sets(Exp)] and the phenotypic performance in various biomass, growth rateand/or vigor components [Correlation vector (corr.)] under normalconditions across Maize accessions. P = p value.

TABLE 99 Correlation between the expression level of selected genes ofsome embodiments of the invention in various tissues and the phenotypicperformance under low nitrogen conditions across Maize accessions Corr.Gene Exp. Corr. Gene Exp. Set Name R P value set Set ID Name R P valueset ID LGP73 0.81 7.64E−03 2 2 LGP73 0.73 2.46E−02 2 1 LGP73 0.916.97E−04 2 4 LGP86 0.70 2.30E−02 1 4 Table 99. Provided are thecorrelations (R) between the expression levels of yield improving genesand their homologues in tissues [Leaves or roots; Expression sets (Exp)]and the phenotypic performance in various biomass, growth rate and/orvigor components [Correlation vector (corr.)] under low nitrogenconditions across Maize accessions. P = p value.

TABLE 100 Correlation between the expression level of selected genes ofsome embodiments of the invention in various tissues and the phenotypicperformance under cold conditions across Maize accessions Gene Exp.Corr. Set Gene Exp. Corr. Set Name R P value set ID Name R P value setID LGP25 0.72 2.79E−02 2 7 LGP25 0.78 1.29E−02 2 1 LGP25 0.75 1.89E−02 26 LGP27 0.77 2.64E−02 1 3 LGP72 0.74 3.65E−02 1 3 LGP89 0.79 1.84E−02 13 LGP92 0.85 6.86E−03 1 5 Table 100. Provided are the correlations (R)between the expression levels of yield improving genes and theirhomologues in tissues [Leaves or roots; Expression sets (Exp)] and thephenotypic performance in various biomass, growth rate and/or vigorcomponents [Correlation vector (corr.)] under cold conditions (10 ± 2°C.) across Maize accessions. P = p value.

TABLE 101 Correlation between the expression level of selected genes ofsome embodiments of the invention in various tissues and the phenotypicperformance under salinity conditions across Maize accessions Gene Exp.Corr. Gene Exp. Corr. Name R P value set Set ID Name R P value set SetID LGP25 0.78 1.27E−02 2 5 LGP25 0.77 1.43E−02 2 1 LGP73 0.71 3.13E−02 22 LGP88 0.75 1.19E−02 1 5 LGP92 0.75 1.31E−02 1 5 Table 101. Providedare the correlations (R) between the expression levels of yieldimproving genes and their homologues in tissues [Leaves or roots;Expression sets (Exp)] and the phenotypic performance in variousbiomass, growth rate and/or vigor components [Correlation vector(corr.)] under salinity conditions (100 mM NaCl) across Maizeaccessions. P = p value.

Example 13 Production of Maize Transcriptome and High ThroughputCorrelation Analysis when Grown Under Normal and Defoliation ConditionsUsing 60K Maize Oligonucleotide Micro-Array

To produce a high throughput correlation analysis, the present inventorsutilized a Maize oligonucleotide micro-array, produced by AgilentTechnologies [chem. (dot) agilent (dot) com/Scripts/PDS (dot)asp?1Page=50879]. The array oligonucleotide represents about 60K Maizegenes and transcripts designed based on data from Public databases(Example 1). To define correlations between the levels of RNA expressionand yield, biomass components or vigor related parameters, various plantcharacteristics of 13 different Maize hybrids were analyzed under normaland defoliation conditions. Same hybrids were subjected to RNAexpression analysis. The correlation between the RNA levels and thecharacterized parameters was analyzed using Pearson correlation test[davidmlane (dot) com/hyperstat/A34739 (dot) html].

Experimental Procedures

13 maize hybrids lines were grown in 6 repetitive plots, in field. Maizeseeds were planted and plants were grown in the field using commercialfertilization and irrigation protocols. After silking 3 plots in everyhybrid line underwent the defoliation treatment. In this treatment allthe leaves above the ear (about 75% of the total leaves) were removed.After the treatment all the plants were grown according to the samecommercial fertilization and irrigation protocols.

Three tissues at flowering developmental (R1) and grain filling (R3)stage including leaf (flowering -R1), stem (flowering -R1 and grainfilling -R3), and flowering meristem (flowering -R1) representingdifferent plant characteristics, were sampled from treated and untreatedplants. RNA was extracted as described in “GENERAL EXPERIMENTAL ANDBIOINFORMATICS METHODS”. For convenience, each micro-array expressioninformation tissue type has received a Set ID as summarized in Tables102-104 below.

TABLE 102 Tissues used for Maize transcriptome expression sets (Undernormal conditions) Expression Set Set ID Female meristem at floweringstage under normal conditions 1 leaf at flowering stage under normalconditions 2 stem at flowering stage under normal conditions 3 stem atgrain filling stage under normal conditions 4 Table 102: Provided arethe identification (ID) numbers of each of the Maize expression sets.

TABLE 103 Tissues used for Maize transcriptome expression sets (Underdefoliation conditions) Expression Set Set ID Female meristem atflowering stage under defoliation conditions 1 leaf at flowering stageunder defoliation conditions 2 stem at flowering stage under defoliationconditions 3 stem at grain filling stage under defoliation conditions 4Table 103: Provided are the identification (ID) numbers of each of theMaize expression sets.

The image processing system was used, which consists of a personaldesktop computer (Intel P4 3.0 GHz processor) and a public domainprogram—ImageJ 1.37, Java based image processing software, which wasdeveloped at the U.S. National Institutes of Health and is freelyavailable on the internet at rsbweb (dot) nih (dot) gov/. Images werecaptured in resolution of 10 Mega Pixels (3888×2592 pixels) and storedin a low compression JPEG (Joint Photographic Experts Group standard)format. Next, image processing output data for seed area and seed lengthwas saved to text files and analyzed using the JMP statistical analysissoftware (SAS institute).

The following parameters were collected by imaging.

1000 grain weight—At the end of the experiment all seeds from all plotswere collected and weighed and the weight of 1000 was calculated.

Ear Area (cm²)—At the end of the growing period 5 ears were photographedand images were processed using the below described image processingsystem. The Ear area was measured from those images and was divided bythe number of ears.

Ear Length and Ear Width (cm)—At the end of the growing period 6 earswere, photographed and images were processed using the below describedimage processing system. The Ear length and width (longest axis) wasmeasured from those images and was divided by the number of ears.

Grain Area (cm²)—At the end of the growing period the grains wereseparated from the ear. A sample of ˜200 grains were weighted,photographed and images were processed using the below described imageprocessing system. The grain area was measured from those images and wasdivided by the number of grains.

Grain Length and Grain width (cm)—At the end of the growing period thegrains were separated from the ear. A sample of ˜200 grains wasweighted, photographed and images were processed using the belowdescribed image processing system. The sum of grain lengths/or width(longest axis) was measured from those images and was divided by thenumber of grains.

Grain Perimeter (cm)—At the end of the growing period the grains wereseparated from the ear. A sample of ˜200 grains was weighted,photographed and images were processed using the below described imageprocessing system. The sum of grain perimeter was measured from thoseimages and was divided by the number of grains.

Ear filled grain area (cm²)—At the end of the growing period 5 ears werephotographed and images were processed using the below described imageprocessing system. The Ear area filled with kernels was measured fromthose images and was divided by the number of Ears.

Filled per Whole Ear—was calculated as the length of the ear with grainsout of the total ear.

Additional parameters were collected either by sampling 6 plants perplot or by measuring the parameter across all the plants within theplot.

Cob width [cm]—The diameter of the cob without grains was measured usinga ruler.

Ear average weight [kg]—At the end of the experiment (when ears wereharvested) total and 6 selected ears per plots were collected. The earswere weighted and the average ear per plant was calculated. The earweight was normalized using the relative humidity to be 0%.

Plant height and Ear height—Plants were characterized for height atharvesting. In each measure, 6 plants were measured for their heightusing a measuring tape. Height was measured from ground level to top ofthe plant below the tassel. Ear height was measured from the groundlevel to the place were the main ear is located

Ear row num—The number of rows per ear was counted.

Ear fresh weight per plant (GF)—During the grain filling period (GF) andtotal and 6 selected ears per plot were collected separately. The earswere weighted and the average ear weight per plant was calculated.

Ears dry weight—At the end of the experiment (when ears were harvested)total and 6 selected ears per plots were collected and weighted. The earweight was normalized using the relative humidity to be 0%.

Ears fresh weight—At the end of the experiment (when ears wereharvested) total and 6 selected ears per plots were collected andweighted.

Ears per plant—number of ears per plant were counted.

Grains weight (Kg.)—At the end of the experiment all ears werecollected. Ears from 6 plants from each plot were separately threshedand grains were weighted.

Grains dry weight (Kg.)—At the end of the experiment all ears werecollected. Ears from 6 plants from each plot were separately threshedand grains were weighted. The grain weight was normalized using therelative humidity to be 0%.

Grain weight per ear (Kg.)—At the end of the experiment all ears werecollected. 5 ears from each plot were separately threshed and grainswere weighted. The average grain weight per ear was calculated bydividing the total grain weight by the number of ears.

Leaves area per plant at GF and HD [LAI, leaf area index]=Total leafarea of 6 plants in a plot his parameter was measured at two time pointsduring the course of the experiment; at heading (HD) and during thegrain filling period (GF). Measurement was performed using a Leafarea-meter at two time points in the course of the experiment; duringthe grain filling period and at the heading stage (VT).

Leaves fresh weight at GF and HD—This parameter was measured at two timepoints during the course of the experiment; at heading (HD) and duringthe grain filling period (GF). Leaves used for measurement of the LAIwere weighted.

Lower stem fresh weight at GF, HD and H—This parameter was measured atthree time points during the course of the experiment: at heading (HD),during the grain filling period (GF) and at harvest (H). Lowerinternodes from at least 4 plants per plot were separated from the plantand weighted. The average internode weight per plant was calculated bydividing the total grain weight by the number of plants.

Lower stem length at GF, HD and H—This parameter was measured at threetime points during the course of the experiment; at heading (HD), duringthe grain filling period (GF) and at harvest (H). Lower internodes fromat least 4 plants per plot were separated from the plant and theirlength was measured using a ruler. The average internode length perplant was calculated by dividing the total grain weight by the number ofplants.

Lower stem width at GF, HD, and H—This parameter was measured at threetime points during the course of the experiment: at heading (HD), duringthe grain filling period (GF) and at harvest (H). Lower internodes fromat least 4 plants per plot were separated from the plant and theirdiameter was measured using a caliber. The average internode width perplant was calculated by dividing the total grain weight by the number ofplants.

Plant height growth—the relative growth rate (RGR) of Plant Height wascalculated as described in Formula III above.

SPAD—Chlorophyll content was determined using a Minolta SPAD 502chlorophyll meter and measurement was performed 64 days post sowing.SPAD meter readings were done on young fully developed leaf. Threemeasurements per leaf were taken per plot. Data were taken after 46 and54 days after sowing (DPS).

Stem fresh weight at GF and HD—This parameter was measured at two timepoints during the course of the experiment: at heading (HD) and duringthe grain filling period (GF). Stems of the plants used for measurementof the LAI were weighted.

Total dry matter—Total dry matter was calculated using Formula XXIabove.

Upper stem fresh weight at GF, HD and H—This parameter was measured atthree time points during the course of the experiment; at heading (HD),during the grain filling period (GF) and at harvest (H). Upperinternodes from at least 4 plants per plot were separated from the plantand weighted. The average internode weight per plant was calculated bydividing the total grain weight by the number of plants.

Upper stem length at GF, HD, and H—This parameter was measured at threetime points during the course of the experiment; at heading (HD), duringthe grain filling period (GF) and at harvest (H). Upper internodes fromat least 4 plants per plot were separated from the plant and theirlength was measured using a ruler. The average internode length perplant was calculated by dividing the total grain weight by the number ofplants.

Upper stem width at GF, HD and H (mm)—This parameter was measured atthree time points during the course of the experiment; at heading (HD),during the grain filling period (GF) and at harvest (H). Upperinternodes from at least 4 plants per plot were separated from the plantand their diameter was measured using a caliber. The average internodewidth per plant was calculated by dividing the total grain weight by thenumber of plants.

Vegetative dry weight (Kg.)—total weight of the vegetative portion of 6plants (above ground excluding roots) after drying at 70° C. in oven for48 hours weight by the number of plants.

Vegetative fresh weight (Kg.)—total weight of the vegetative portion of6 plants (above ground excluding roots).

Node number—nodes on the stem were counted at the heading stage of plantdevelopment.

TABLE 104 Maize correlated parameters (vectors) under normal grownconditions and under the treatment of defoliation Normal conditionsDefoliation Correlation Correlation Correlated parameter with IDCorrelated parameter with ID 1000 grain weight [g] 1 1000 grain weight 1Avr internode length 2 Avr_internode_length 2 Cob width [mm] 3 Cob width3 Ear Area [cm²] 4 Ear Area (cm²) 4 Ear filled grain area [cm²] 5 Earfilled grain area 5 Ear Width [cm] 6 Ear Width 6 Ear average weight [g]7 Ear average weight 7 Ear height [cm] 8 Ear height 8 Ear length [cm] 9Ear length 9 Ear row num 10 Ear row num 10 Ear fresh weight per plant(GF) 11 Ears dry weight 11 [g/plant] Ears dry weight [kg] 12 Ears freshweight 12 Ears fresh weight [kg] 13 Ears per plant 13 Ears per plant[number] 14 Filled per Whole Ear 14 Filled per Whole Ear [value] 15Grain Perimeter 15 Grain Perimeter [cm] 16 Grain area [cm²] 16 Grainarea [cm²] 17 Grain length 17 Grain length [cm] 18 Grain_width 18 Grainwidth [cm] 19 Grains dry weight 19 Grains dry weight [kg] 20 Grainsweight 20 Grains weight [kg] 21 Grain weight per ear 21 Grain weight perear [kg] 22 Harvest_index 22 Harvest index 23 Leaves fresh weight (HD)23 Leaves fresh weight (GF) [g] 24 Leaves area per plant (hd) 24 Leavesfresh weight (HD) [g] 25 Leaves temperature (GF) 25 Leaves area perplant (GF) [cm²] 26 Lower stem fresh weight 26 (H) Leaves area per plant(HD) [cm²] 27 Lower stem fresh weight 27 (HD) Leaves temperature (GF) 28Lower stem length (H) 28 Lower stem fresh weight (GF) [g] 29 Lower stemlength (HD) 29 Lower stem fresh weight (H) [g] 30 Lower stem width (H)30 Lower stem fresh weight (HD) [g] 31 Lower stem width (HD) 31 Lowerstem length (GF) [cm] 32 Node number 32 Lower stem length (H) [cm] 33Plant height 33 Lower stem length (HD) [cm] 34 Plant height growth 34Lower stem width (GF) [mm] 35 SPAD (GF) 35 Lower stem width (H) 36 Stemfresh weight (HD) 36 Lower stem width (HD) [mm] 37 Total dry matter 37Node_number 38 Upper stem fresh weight 38 (H) Plant height [cm] 39 Upperstem length (H) 39 Plant height growth [cm/day] 40 Upper stem width (H)40 SPAD (GF) [value] 41 Vegetative dry weight 41 Stem fresh weight (GF)[g] 42 Vegetative fresh weight 42 Stem fresh weight (HD) [g] 43 Totaldry matter [kg] 44 Upper stem fresh weight (GF) [g] 45 Upper stem freshweight (H) [g] 46 Upper stem length (GF) [cm] 47 Upper stem length (H)[cm] 48 Upper stem width (GF) [mm] 49 Upper stem width (H) [mm] 50Vegetative dry weight [kg] 51 Vegetative fresh weight [kg] 52 Table 104.

Thirteen maize varieties were grown, and characterized for parameters,as described above. The average for each parameter was calculated usingthe JMP software, and values are summarized in Tables 105-108 below.Subsequent correlation between the various transcriptome sets for all orsub set of lines was done by the bioinformatic unit and results wereintegrated into the database (Tables 109 and 110 below).

TABLE 105 Measured parameters in Maize Hybrid under normal conditionsEcotype/Treatment Line-1 Line-2 Line-3 Line-4 Line-5 Line-6 Line-7 1296.50 263.25 303.61 304.70 281.18 330.45 290.88 2 17.44 17.61 18.5519.18 18.66 19.52 17.11 3 24.63 25.11 23.21 23.69 22.81 22.40 23.18 482.30 74.63 77.00 90.15 83.80 96.63 78.36 5 80.89 72.42 73.43 85.9680.64 95.03 74.41 6 4.66 4.79 4.96 5.00 4.65 4.80 4.79 7 209.50 164.63177.44 218.53 205.58 135.77 147.49 8 121.67 134.24 149.64 152.14 143.83133.65 118.39 9 22.09 19.62 20.02 23.21 22.63 23.74 20.31 10 13.00 14.9414.56 14.56 13.56 13.06 16.12 11 351.26 323.08 307.87 330.60 320.51434.60 325.08 12 1.26 1.09 1.06 1.31 1.23 1.35 1.16 13 1.69 1.46 1.411.70 1.52 1.74 1.80 14 1.000 1.111 1.000 1.000 1.000 1.056 1.000 150.982 0.969 0.953 0.953 0.949 0.937 0.930 16 3.30 3.23 3.28 3.34 3.183.38 3.25 17 0.72 0.67 0.71 0.72 0.67 0.75 0.66 18 1.12 1.12 1.13 1.171.08 1.16 1.14 19 0.81 0.75 0.79 0.78 0.79 0.82 0.74 20 0.91 0.80 0.770.92 0.83 0.99 0.82 21 1.04 0.91 0.87 1.06 0.95 1.12 0.94 22 0.15 0.130.13 0.15 0.14 0.16 0.14 23 0.35 0.39 0.33 0.38 0.35 0.39 0.36 24 230.13197.64 201.03 205.53 224.81 204.49 212.41 25 110.97 80.57 157.21 128.83100.57 111.80 116.75 26 7034.60 6402.80 6353.07 6443.92 6835.50 6507.337123.48 27 4341.25 3171.00 4205.50 4347.50 3527.00 4517.33 3984.78 2833.11 33.52 33.87 34.18 33.78 32.85 33.19 29 35.40 25.03 26.51 21.7426.13 34.44 27.61 30 23.52 20.34 25.08 14.18 17.53 25.74 20.60 31 72.9959.90 74.72 90.48 69.52 66.91 60.36 32 19.35 20.40 20.93 21.38 20.0320.31 18.08 33 16.76 20.02 22.59 21.68 22.34 21.39 17.07 34 14.50 17.7520.00 19.35 20.33 20.75 15.00 35 19.86 16.84 16.14 16.37 17.01 17.5318.11 36 19.42 17.19 16.09 16.92 17.52 17.88 17.96 37 24.14 20.53 20.9724.43 21.70 19.49 23.47 38 15.22 14.56 14.61 14.83 15.00 13.83 14.28 39265.11 255.94 271.11 283.89 279.72 268.78 244.25 40 5.43 5.59 6.15 5.996.37 6.47 4.82 41 59.77 53.17 53.21 54.95 53.99 55.24 55.38 42 649.03489.32 524.06 512.66 542.16 627.76 507.78 43 758.61 587.88 801.32 794.80721.87 708.38 660.70 44 2.57 2.06 2.32 2.44 2.36 2.57 2.23 45 19.6115.54 17.82 10.79 14.41 20.31 15.85 46 12.94 11.21 12.98 6.50 7.99 12.089.72 47 16.63 18.75 18.38 17.92 17.60 18.79 17.07 48 16.93 18.76 18.7220.01 19.40 19.65 16.42 49 16.00 14.11 13.50 11.89 13.08 14.34 15.04 5014.93 13.00 12.44 12.04 12.89 13.28 13.10 51 1.31 0.97 1.25 1.13 1.131.21 1.07 52 3.16 2.25 2.61 2.60 2.42 2.64 2.22

TABLE 106 Measured parameters in Maize Hybrid under normal conditions,additional maize lines Ecotype/Treatment Line-8 Line-9 Line-10 Line-11Line-12 Line-13 1 250.26 306.20 253.19 277.03 269.53 274.81 2 18.5917.72 20.63 17.96 17.36 19.28 3 24.88 26.47 23.09 22.69 23.55 26.31 493.91 96.77 85.44 76.77 NA 97.99 5 92.31 95.43 83.28 74.35 NA 96.88 65.18 5.00 4.95 4.79 NA 5.43 7 207.11 228.44 215.92 198.69 188.50 254.428 145.24 133.78 143.71 134.17 143.00 147.78 9 22.60 23.84 21.74 20.04 NA22.41 10 15.89 14.00 15.44 14.89 14.94 16.78 11 327.15 363.70 405.72338.24 345.32 369.69 12 1.29 1.37 1.30 1.19 1.13 1.53 13 1.60 1.74 1.681.56 1.42 1.89 14 1.056 1.000 1.000 1.000 1.000 1.000 15 0.982 0.9860.974 0.966 NA 0.989 16 3.18 3.29 3.27 3.22 3.15 3.38 17 0.65 0.70 0.680.67 0.65 0.72 18 1.12 1.15 1.16 1.12 1.09 1.21 19 0.73 0.77 0.74 0.760.76 0.76 20 0.92 1.02 0.94 0.85 0.81 1.14 21 1.05 1.15 1.08 0.97 0.921.29 22 0.15 0.17 0.16 0.14 0.14 0.19 23 0.33 0.44 0.39 0.39 0.39 0.4024 181.43 199.22 206.91 168.54 199.42 200.12 25 106.95 85.97 102.71105.73 102.12 143.06 26 6075.21 6597.67 6030.40 6307.06 6617.65 6848.0327 3696.75 3926.67 3127.67 3942.75 3955.00 4854.00 28 33.66 33.78 32.6433.95 33.28 33.90 29 25.26 26.18 34.31 25.50 23.06 25.59 30 16.35 18.9027.30 22.35 19.26 22.82 31 63.07 55.89 82.13 60.02 58.70 116.12 32 20.1819.81 22.89 19.81 19.53 21.40 33 20.69 18.48 23.31 19.39 19.66 19.97 3418.68 20.50 22.57 19.83 14.50 20.33 35 17.09 16.87 17.49 16.62 17.1017.38 36 18.42 17.43 18.07 17.68 17.61 18.93 37 20.97 21.46 21.41 22.1223.25 24.31 38 14.72 15.44 14.33 14.44 14.89 14.39 39 273.56 273.22295.33 259.25 257.89 277.19 40 6.01 5.99 6.66 5.99 5.62 6.53 41 56.7655.81 58.54 51.68 55.16 54.16 42 549.34 509.74 662.13 527.43 474.68544.03 43 724.58 618.46 837.56 612.81 728.00 950.29 44 2.73 2.33 2.402.20 2.08 2.84 45 14.39 17.85 20.42 13.93 13.05 16.45 46 6.98 9.40 13.589.20 7.69 10.17 47 17.52 18.15 18.61 17.69 18.15 18.64 48 18.34 16.6319.38 16.71 16.27 15.92 49 13.63 14.73 14.61 13.17 12.77 14.15 50 13.4813.42 13.27 13.14 12.53 13.79 51 1.44 0.96 1.10 1.01 0.95 1.31 52 2.902.22 2.83 2.29 2.15 2.90

TABLE 107 Measured parameters in Maize Hybrid under defoliationEcotype/Treatment Line-1 Line-2 Line-3 Line-4 Line-5 Line-6 Line-7 1280.03 251.86 294.29 295.36 288.40 308.25 230.12 2 16.60 17.30 17.9118.88 19.27 18.41 17.72 3 19.03 22.12 16.31 21.54 19.84 18.21 19.77 453.60 45.50 38.31 58.47 53.89 63.54 39.83 5 51.50 42.95 34.59 55.6751.36 61.44 36.31 6 4.18 4.21 3.92 4.77 4.51 4.61 4.10 7 89.20 100.7573.39 129.84 129.78 115.06 85.04 8 119.44 131.56 145.53 156.06 145.28129.53 123.38 9 16.34 13.63 12.89 15.94 15.34 17.53 13.21 10 12.71 14.3613.00 14.12 13.47 13.07 14.06 11 0.75 0.58 0.44 0.74 0.78 0.58 0.45 120.97 0.83 0.63 0.98 1.01 0.80 0.65 13 1.00 0.94 1.00 0.94 1.00 0.94 0.8914 0.954 0.915 0.873 0.950 0.948 0.961 0.905 15 3.109 3.144 3.179 3.2073.196 3.230 3.130 16 0.649 0.632 0.669 0.675 0.677 0.683 0.631 17 1.0521.080 1.079 1.110 1.087 1.094 1.066 18 0.777 0.740 0.781 0.765 0.7860.788 0.750 19 0.52 0.40 0.29 0.52 0.55 0.40 0.30 20 0.60 0.46 0.33 0.590.62 0.46 0.35 21 0.09 0.07 0.05 0.09 0.09 0.08 0.06 22 0.34 0.28 0.210.33 0.35 0.26 0.22 23 112.27 94.99 125.14 144.48 112.50 116.16 113.7824 3914.00 3480.00 4276.50 4985.50 4643.50 4223.00 3436.00 25 32.4733.09 33.64 32.29 32.87 33.40 33.43 26 23.02 26.50 26.98 15.24 18.1937.21 27.88 27 64.16 53.81 56.41 80.95 71.27 66.69 64.19 28 16.29 21.4420.85 22.58 22.94 21.62 18.76 29 15.15 18.50 16.67 18.07 18.00 19.8316.10 30 19.54 16.90 15.79 17.01 17.12 18.17 18.21 31 24.30 20.57 21.0624.87 20.85 20.46 20.96 32 15.17 14.39 15.00 15.11 14.50 14.22 14.39 33251.42 248.64 268.06 285.11 278.83 261.88 254.64 34 6.38 6.32 6.31 6.936.83 7.14 6.48 35 61.21 57.36 58.02 62.36 60.72 62.22 59.65 36 713.54538.04 705.53 803.33 703.36 664.23 673.24 37 1.54 1.37 1.44 1.53 1.571.57 1.34 38 8.68 11.08 14.10 4.89 6.04 13.95 10.93 39 16.24 18.83 17.7419.64 20.74 20.14 17.18 40 14.27 12.82 12.69 11.09 12.00 13.03 14.25 410.79 0.78 1.00 0.79 0.79 1.00 0.88 42 2.51 1.96 2.80 2.11 2.20 2.79 2.54

TABLE 108 Measured parameters in Maize Hybrid under defoliation,additional maize lines Ecotype/Treatment Line-8 Line-9 Line-10 Line-11Line-12 Line-13 1 271.25 259.43 243.98 262.41 248.64 244.16 2 17.8817.26 18.94 18.69 18.25 19.97 3 22.44 20.28 19.64 22.32 23.31 27.78 447.33 65.90 43.83 43.28 52.30 58.31 5 43.34 64.80 39.56 40.43 49.2855.69 6 4.20 4.66 4.06 4.01 4.41 4.98 7 33.10 161.76 89.36 87.68 88.18124.58 8 135.00 136.50 136.39 130.32 139.71 143.44 9 14.82 17.60 13.7813.75 15.53 14.87 10 13.75 13.94 12.79 13.00 14.29 15.83 11 0.63 0.800.54 0.55 0.51 0.75 12 0.82 1.15 0.88 0.79 0.69 0.99 13 1.00 0.88 1.001.06 0.94 1.00 14 0.905 0.983 0.890 0.918 0.940 0.950 15 3.016 3.1173.086 3.030 2.976 3.153 16 0.610 0.623 0.619 0.600 0.583 0.631 17 1.0241.084 1.054 1.025 0.995 1.095 18 0.750 0.724 0.741 0.738 0.733 0.725 190.44 0.67 0.36 0.38 0.34 0.53 20 0.50 0.77 0.41 0.43 0.39 0.61 21 0.070.12 0.06 0.06 0.06 0.09 22 0.28 0.38 0.24 0.29 0.23 0.31 23 93.74 89.8686.98 117.27 150.68 161.65 24 4593.00 4315.50 4020.50 4154.00 4851.503750.00 25 33.42 33.98 33.12 32.64 33.55 33.27 26 17.33 20.51 25.3628.41 23.16 38.80 27 76.23 57.85 69.98 67.30 72.90 83.58 28 20.88 17.8320.70 20.43 20.11 24.13 29 14.83 17.50 23.67 19.00 16.45 20.60 30 17.2317.88 17.12 17.53 18.63 19.87 31 22.47 21.23 19.85 21.29 23.58 21.37 3214.67 15.61 14.39 14.06 14.61 14.00 33 261.94 268.88 272.71 262.50266.33 279.14 34 6.28 7.04 7.20 7.34 6.94 7.27 35 59.99 56.76 65.7057.94 60.31 57.71 36 738.37 692.23 619.79 729.23 794.64 847.52 37 1.471.66 1.48 1.31 1.48 1.71 38 6.48 9.01 10.69 10.38 8.49 12.29 39 19.1216.74 15.96 17.31 18.19 17.77 40 12.77 13.52 13.08 13.43 13.21 14.72 410.84 0.86 0.94 0.76 0.96 0.97 42 2.48 2.35 2.59 2.41 2.70 2.72

Tables 109 and 110 hereinbelow provide the correlations (R) between theexpression levels yield improving genes and their homologs in varioustissues [Expression (Exp) sets] and the phenotypic performance [yield,biomass, growth rate and/or vigor components (Correlation vector(Corr.))] under normal and defoliation conditions across maizevarieties. P=p value.

TABLE 109 Correlation between the expression level of selected genes ofsome embodiments of the invention in various tissues and the phenotypicperformance under normal conditions across maize varieties Gene Exp.Corr. Gene Exp. Corr. Name R P value set Set ID Name R P value set IDLGP25 0.75 3.33E−03 1 45 LGP25 0.72 5.13E−03 1 11 LGP25 0.74 5.65E−03 321 LGP25 0.75 5.40E−03 3 12 LGP25 0.83 9.13E−04 3 43 LGP25 0.80 1.68E−033 31 LGP25 0.75 5.38E−03 3 22 LGP25 0.75 5.38E−03 3 20 LGP25 0.721.30E−02 4 21 LGP25 0.70 1.57E−02 4 43 LGP25 0.73 1.02E−02 4 45 LGP250.86 6.67E−04 4 11 LGP25 0.72 1.29E−02 4 22 LGP25 0.72 1.29E−02 4 20LGP25 0.71 1.48E−02 2 11 LGP27 0.72 7.70E−03 3 29 LGP27 0.80 1.84E−03 345 LGP27 0.84 6.86E−04 3 46 LGP27 0.75 7.62E−03 2 45 LGP27 0.74 9.39E−032 17 LGP27 0.73 1.09E−02 2 16 LGP27 0.83 1.56E−03 2 11 LGP72 0.721.21E−02 4 34 LGP72 0.75 7.83E−03 4 33 LGP72 0.83 1.50E−03 4 48 LGP730.72 8.51E−03 3 40 LGP73 0.71 1.02E−02 3 34 LGP73 0.80 1.87E−03 3 39LGP73 0.71 1.48E−02 4 10 LGP73 0.90 1.49E−04 4 3 LGP73 0.71 1.52E−02 432 LGP73 0.73 1.09E−02 4 2 LGP73 0.76 6.28E−03 2 47 LGP73 0.71 1.41E−022 11 LGP74 0.75 3.29E−03 1 3 LGP74 0.87 9.50E−05 1 7 LGP74 0.81 1.32E−031 15 LGP74 0.72 1.28E−02 4 21 LGP74 0.72 1.19E−02 4 31 LGP74 0.766.92E−03 4 18 LGP74 0.73 1.56E−02 4 6 LGP74 0.73 1.06E−02 4 22 LGP740.73 1.06E−02 4 20 LGP74 0.73 1.64E−02 2 9 LGP74 0.74 1.38E−02 2 6 LGP750.74 5.59E−03 3 2 LGP82 0.78 4.80E−03 4 32 LGP86 0.75 7.37E−03 4 43LGP86 0.84 1.07E−03 2 45 LGP86 0.76 7.16E−03 2 30 LGP86 0.81 2.48E−03 211 LGP86 0.74 9.22E−03 2 46 LGP87 0.75 4.72E−03 3 33 LGP87 0.72 8.91E−033 47 LGP87 0.71 9.32E−03 3 48 LGP87 0.80 1.77E−03 3 32 LGP87 0.755.20E−03 3 2 LGP87 0.84 1.29E−03 4 10 LGP87 0.75 7.96E−03 2 21 LGP870.72 1.97E−02 2 5 LGP87 0.76 7.10E−03 2 22 LGP87 0.76 7.10E−03 2 20LGP88 0.75 4.89E−03 3 43 LGP88 0.74 8.97E−03 3 6 LGP88 0.75 7.64E−03 411 LGP89 0.73 1.08E−02 4 21 LGP89 0.73 1.02E−02 4 43 LGP89 0.78 5.03E−034 31 LGP89 0.81 2.29E−03 4 18 LGP89 0.72 1.29E−02 4 2 LGP89 0.731.05E−02 4 11 LGP89 0.73 1.05E−02 4 22 LGP89 0.73 1.05E−02 4 20 LGP900.91 3.04E−05 3 21 LGP90 0.90 5.43E−05 3 12 LGP90 0.72 8.49E−03 3 39LGP90 0.72 8.14E−03 3 43 LGP90 0.77 5.82E−03 3 5 LGP90 0.75 4.93E−03 331 LGP90 0.84 6.59E−04 3 18 LGP90 0.77 5.45E−03 3 4 LGP90 0.76 4.40E−033 16 LGP90 0.70 1.09E−02 3 32 LGP90 0.72 8.41E−03 3 2 LGP90 0.914.16E−05 3 22 LGP90 0.91 4.16E−05 3 20 LGP91 0.71 9.82E−03 3 43 LGP910.75 5.23E−03 3 25 LGP91 0.78 4.45E−03 4 43 LGP91 0.74 9.48E−03 4 31LGP92 0.77 5.88E−03 3 15 LGP92 0.79 2.22E−03 3 52 LGP94 0.72 1.22E−02 443 LGP95 0.72 8.44E−03 3 48 LGP95 0.88 3.26E−04 4 14 LGP95 0.77 9.60E−032 5 LGP95 0.78 4.38E−03 2 47 LGP95 0.76 1.04E−02 2 9 LGP95 0.76 1.00E−022 4 LGP95 0.78 7.60E−03 2 6

TABLE 10 Correlation between the expression level of selected genes ofsome embodiments of the invention in various tissues and the phenotypicperformance under normal defoliation across maize varieties Gene Exp.Corr. Gene Exp. Corr. Name R P value set Set ID Name R P value set SetID LGP25 0.77 5.16E−03 4 30 LGP25 0.72 1.24E−02 4 42 LGP27 0.74 6.01E−032 38 LGP27 0.78 3.07E−03 2 26 LGP27 0.76 6.58E−03 4 30 LGP72 0.801.68E−03 1 21 LGP72 0.72 7.96E−03 1 20 LGP72 0.71 9.99E−03 1 11 LGP720.73 6.65E−03 1 22 LGP72 0.72 8.14E−03 1 19 LGP72 0.81 1.30E−03 3 39LGP72 0.79 2.27E−03 3 28 LGP72 0.75 5.19E−03 3 1 LGP72 0.71 9.03E−03 3 2LGP73 0.71 9.34E−03 1 42 LGP73 0.74 5.68E−03 1 41 LGP73 0.74 5.87E−03 134 LGP73 0.71 9.06E−03 3 16 LGP73 0.74 5.85E−03 3 18 LGP73 0.78 2.88E−032 3 LGP74 0.70 1.07E−02 2 17 LGP74 0.75 7.38E−03 4 38 LGP74 0.748.95E−03 4 40 LGP74 0.90 1.43E−04 4 30 LGP74 0.88 3.82E−04 4 26 LGP820.71 1.00E−02 3 39 LGP82 0.73 7.37E−03 3 28 LGP82 0.84 1.14E−03 4 3LGP82 0.78 4.59E−03 4 10 LGP82 0.75 7.39E−03 4 26 LGP86 0.73 6.72E−03 339 LGP86 0.81 2.66E−03 4 31 LGP87 0.77 3.63E−03 2 26 LGP87 0.71 1.40E−024 11 LGP88 0.70 1.64E−02 4 37 LGP88 0.74 9.78E−03 4 41 LGP89 0.792.02E−03 3 35 LGP90 0.80 1.98E−03 1 3 LGP91 0.78 3.00E−03 3 23 LGP910.78 2.97E−03 3 36 LGP91 0.73 7.20E−03 3 27 LGP91 0.77 5.40E−03 4 36LGP91 0.91 1.11E−04 4 30 LGP91 0.76 7.22E−03 4 42 LGP94 0.71 9.99E−03 323 LGP94 0.76 4.11E−03 2 30 LGP94 0.85 9.61E−04 4 30 LGP94 0.71 1.48E−024 31 LGP95 0.83 9.53E−04 1 29 LGP95 0.82 1.18E−03 2 29 LGP95 0.854.31E−04 2 26

Example 14 Production of Maize Transcriptome and High ThroughputCorrelation Analysis with Yield and NUE Related Parameters Using 60KMaize Oligonucleotide Micro-Arrays

In order to produce a high throughput correlation analysis between plantphenotype and gene expression level, the present inventors utilized amaize oligonucleotide micro-array, produced by Agilent Technologies[chem. (dot) agilent (dot) com/Scripts/PDS (dot) asp?1Page=50879]. Thearray oligonucleotide represents about 60,000 maize genes andtranscripts.

Correlation of Maize Hybrids Across Ecotypes Grown Under Low NitrogenConditions

Experimental Procedures

12 Maize hybrids were grown in 3 repetitive plots in field. Maize seedswere planted and plants were grown in the field using commercialfertilization and irrigation protocols, which included 485 m³ water perdunam per entire growth period and fertilization of 30 units of nitrogen(using URAN® 21% fertilization) per dunam per entire growth period(normal conditions) or under low nitrogen conditions which included 50%percent less Nitrogen as compared to the amount of nitrogen providedunder the normal conditions. In order to define correlations between thelevels of RNA expression with NUE and yield components or vigor relatedparameters the 12 different maize hybrids were analyzed. Among them, 11hybrids encompassing the observed variance were selected for RNAexpression analysis. The correlation between the RNA levels and thecharacterized parameters was analyzed using Pearson correlation test[davidmlane (dot) com/hyperstat/A34739 (dot) html].

Analyzed Maize tissues—All 10 selected maize hybrids were sampled pereach treatment (low N and normal conditions), in three time points(TP2=V6-V8 (six to eight collar leaf are visible, rapid growth phase andkernel row determination begins), TP5=R1-R2 (silking-blister), TP6=R3-R4(milk-dough). Four types of plant tissues [Ear, flag leaf indicated inTable as leaf, grain distal part, and internode] were sampled and RNAwas extracted as described above. Each micro-array expressioninformation tissue type has received a Set ID as summarized in Tables111-112 below.

TABLE 111 Maize transcriptome expression sets under low nitrogenconditions Expression Set Set ID Maize field Low N/Ear/TP5 1 Maize fieldLow N/Ear/TP6 2 Maize field Low N/Internodes/TP2 3 Maize field LowN/Internodes/TP5 4 Maize field Low N/Internodes/TP6 5 Maize field LowN/Leaf/TP2 6 Maize field Low N/Leaf/TP5 7 Maize field Low N/Leaf/TP6 8Table 111: Provided are the maize transcriptome expression sets underlow nitrogen conditions Leaf = the leaf below the main ear; Flowermeristem = Apical meristem following male flower initiation; Ear = thefemale flower at the anthesis day. Grain Distal = maize developinggrains from the cob extreme area, Grain Basal = maize developing grainsfrom the cob basal area; Internodes = internodes located above and belowthe main ear in the plant.

TABLE 112 Maize transcriptome expression sets under normal growthconditions Expression Set Set ID Maize field Normal/Ear/R1-R2 1 Maizefield Normal/Grain Distal/R4-R5 2 Maize field Normal/Internode/R3-R4 3Maize field Normal/Leaf/R1-R2 4 Maize field Normal/Ear/R3-R4 5 Maizefield Normal/Internode/R1-R2 6 Maize field Normal/Internode/V6-V8 7Maize field Normal/Leaf/V6-V8 8 Table 112: Provided are the maizetranscriptome expression sets under normal growth conditions. Leaf = theleaf below the main ear; Flower meristem = Apical meristem followingmale flower initiation; Ear = the female flower at the anthesis day.Grain Distal = maize developing grains from the cob extreme area, GrainBasal = maize developing grains from the cob basal area; Internodes =internodes located above and below the main ear in the plant.

The following parameters were collected using digital imaging system:

Grain Area (cm²)—At the end of the growing period the grains wereseparated from the ear. A sample of ˜200 grains were weighted,photographed and images were processed using the below described imageprocessing system. The grain area was measured from those images and wasdivided by the number of grains.

Grain Length and Grain width (cm)—At the end of the growing period thegrains were separated from the ear. A sample of ˜200 grains wereweighted, photographed and images were processed using the belowdescribed image processing system. The sum of grain lengths/or width(longest axis) was measured from those images and was divided by thenumber of grains.

Ear Area (cm²)—At the end of the growing period 5 ears were photographedand images were processed using the below described image processingsystem. The Ear area was measured from those images and was divided bythe number of Ears.

Ear Length and Ear Width (cm)—At the end of the growing period 5 earswere photographed and images were processed using the below describedimage processing system. The Ear length and width (longest axis) wasmeasured from those images and was divided by the number of ears.

The image processing system was used, which consists of a personaldesktop computer (Intel P4 3.0 GHz processor) and a public domainprogram—ImageJ 1.37, Java based image processing software, which wasdeveloped at the U.S. National

Institutes of Health and is freely available on the internet at rsbweb(dot) nih (dot) gov/. Images were captured in resolution of 10 MegaPixels (3888×2592 pixels) and stored in a low compression JPEG (JointPhotographic Experts Group standard) format. Next, image processingoutput data for seed area and seed length was saved to text files andanalyzed using the JMP statistical analysis software (SAS institute).

Additional parameters were collected either by sampling 6 plants perplot or by measuring the parameter across all the plants within theplot.

Normalized Grain Weight per plant (gr.)—At the end of the experiment allears from plots within blocks A-C were collected. Six ears wereseparately threshed and grains were weighted, all additional ears werethreshed together and weighted as well. The average grain weight per earwas calculated by dividing the total grain weight by number of totalears per plot (based on plot). In case of 6 ears, the total grainsweight of 6 ears was divided by 6.

Ear FW (gr.)—At the end of the experiment (when ears were harvested)total and 6 selected ears per plots within blocks A-C were collectedseparately. The plants (total and 6) were weighted (gr.) separately andthe average ear per plant was calculated for total (Ear FW per plot) andfor 6 (Ear FW per plant).

Plant height and Ear height—Plants were characterized for height atharvesting. In each measure, 6 plants were measured for their heightusing a measuring tape. Height was measured from ground level to top ofthe plant below the tassel. Ear height was measured from the groundlevel to the place were the main ear is located.

Leaf number per plant—Plants were characterized for leaf number duringgrowing period at 5 time points. In each measure, plants were measuredfor their leaf number by counting all the leaves of 3 selected plantsper plot.

Relative Growth Rate was calculated using Formulas II-XIII, XXVIII,and/or XXXIV (described above).

SPAD—Chlorophyll content was determined using a Minolta SPAD 502chlorophyll meter and measurement was performed at early stages of grainfilling (R1-R2) and late stage of grain filling (R3-R4). SPAD meterreadings were done on young fully developed leaf. Three measurements perleaf were taken per plot. Data were taken after 46 and 54 days aftersowing (DPS).

Dry weight per plant—At the end of the experiment (when inflorescencewere dry) all vegetative material from plots within blocks A-C werecollected.

Dry weight=total weight of the vegetative portion above ground(excluding roots) after drying at 70° C. in oven for 48 hours.

Harvest Index (HI) (Maize)—The harvest index per plant was calculatedusing Formula XVII above.

Percent Filled Ear [%]—it was calculated as the percentage of the Eararea with grains out of the total ear.

Cob diameter [cm]—The diameter of the cob without grains was measuredusing a ruler.

Kernel Row Number per Ear—The number of rows in each ear was counted.

Experimental Results

11 different maize hybrids were grown and characterized for differentparameters. Tables 111-112 describe the Maize expression sets, andTables 113-114 below describe the Maize correlated parameters. Theaverage for each of the measured parameters was calculated using the JMPsoftware (Tables 115-118) and a subsequent correlation analysis wasperformed (Table 119-120). Results were then integrated to the database.

TABLE 113 Maize correlated parameters (vectors) under low nitrogenconditions Correlation Correlated parameter with ID Ear Length [cm] LowN 1 Ear Length of filled area [cm] Low N 2 Ear width [mm] Low N 3 FinalLeaf Number [number] Low N 4 Final Main Ear Height [cm] Low N 5 FinalPlant Height [cm] Low N 6 No of rows per ear [number] Low N 7 SPAD atR1-R2 [number] Low N 8 SPAD at R3-R4 [number] Low N 9 Stalk width at TP5[cm] Low N 10 Ears weight per plot [kg] Low N 11 Final Plant DW [kg] LowN 12 Final Leaf Area [number] Low N 13 NUE yield kg/N applied in soil kgLow N 14 NUE at early grain filling [R1-R2] yield kg/N in plant per 15SPAD Low N NUE at grain filling [R3-R4] yield kg/N in plant per 16 SPADLow N NUpE [biomass/N applied] Low N 17 Seed yield per dunam [kg] Low N18 Yield/LAI [Kg/cm²] Low N 19 Yield/stalk width [Kg/cm] Low N 20 seedyield per plant [kg] Low N 21 Table 113. “cm” = centimeters' “mm” =millimeters; “kg” = kilograms; SPAD at R1-R2 and SPAD R3-R4: Chlorophylllevel after early and late stages of grain filling; “NUE” = nitrogen useefficiency; “NUpE” = nitrogen uptake efficiency; “LAI” = leaf area; “N”= nitrogen; Low N = under low Nitrogen conditions; “Normal” = undernormal conditions; “dunam” = 1000 m².

TABLE 114 Maize correlated parameters (vectors) under normal conditionsCorrelation Correlated parameter with ID Final Plant DW [kg] Normal 1Ear Length [cm] Normal 2 Ear Length of filled area [cm] Normal 3 Earwidth [mm] Normal 4 Final Leaf Number [number] Normal 5 Final Main EarHeight [cm] Normal 6 Final Plant Height [cm] Normal 7 No of rows per ear[number] Normal 8 SPAD at R1-R2 [number] Normal 9 SPAD at R3-R4 [number]Normal 10 Stalk width at TP5 Normal 11 Ears weight per plot [kg] Normal12 Final Leaf Area [number] Normal 13 NUE yield kg/N applied in soil kgNormal 14 NUE at early grain filling [R1-R2] yield kg/N in plant per 15SPAD Normal NUE at grain filling [R3-R4] yield kg/N in plant per 16 SPADNormal NUpE [biomass/N applied] Normal 17 Seed yield per dunam [kg]Normal 18 Yield/LAI Normal 19 Yield/stalk width Normal 20 seed yield perplant [kg] Normal 21 Table 114. “cm” = centimeters' “mm” = millimeters;“kg” = kilograms; SPAD at R1-R2 and SPAD R3-R4: Chlorophyll level afterearly and late stages of grain filling; “NUE” = nitrogen use efficiency;“NUpE” = nitrogen uptake efficiency; “LAI” = leaf area; “N” = nitrogen;Low N = under low Nitrogen conditions; “Normal” = under normalconditions; “dunam” = 1000 m².

TABLE 115 Measured parameters in Maize accessions under Low nitrogenconditions Ecotype/Treatment Line-1 Line-2 Line-3 Line-4 Line-5 Line-6 120.61 20.98 20.22 20.11 20.11 18.50 2 18.40 18.42 19.78 18.83 16.2216.00 3 46.71 48.22 48.32 49.86 52.87 47.44 4 15.02 11.64 13.50 11.6111.83 11.89 5 158.08 136.24 128.39 133.06 137.83 99.56 6 305.84 270.93290.61 252.17 260.22 227.22 7 14.18 15.21 15.00 15.67 16.00 15.94 860.24 57.94 58.76 59.48 58.50 64.04 9 59.29 57.62 58.40 59.19 58.1962.67 10 2.76 2.42 2.65 2.77 2.67 2.59 11 6.61 7.97 9.63 9.22 7.63 7.2112 1.59 1.43 1.53 1.95 1.48 1.60 14 7.22 8.41 10.33 9.99 7.63 7.73 1518.02 21.79 26.33 25.14 19.55 18.05 16 18.35 21.92 26.48 25.33 19.6918.54 17 0.011 0.010 0.010 0.013 0.010 0.011 18 1083.75 1261.63 1549.241497.86 1143.85 1159.26 20 416.53 528.38 583.46 541.02 428.09 444.29 210.14 0.16 0.19 0.19 0.14 0.14 13 2.92 3.15 3.33 2.87 2.79 3.76 19 341.50408.09 464.77 522.26 439.53 312.58 Table 115. Provided are the values ofeach of the parameters (as described above) measured in maize accessions(line) under low nitrogen growth conditions. Growth conditions arespecified in the experimental procedure section.

TABLE 116 Additional parameters in Maize accessions under Low nitrogenconditions Ecotype/Treatment Line-7 Line-8 Line-9 Line-10 Line-11 119.06 18.25 20.10 17.81 21.25 2 15.28 15.69 16.77 14.06 19.56 3 49.6148.57 52.41 42.63 50.00 4 12.56 11.67 12.44 9.28 13.17 5 130.17 114.61143.86 61.61 114.44 6 271.72 248.61 279.33 171.28 269.78 7 15.56 14.5016.41 14.37 15.74 8 56.42 60.00 58.32 53.06 61.72 9 61.04 59.87 57.4749.61 61.87 10 2.98 2.61 2.65 2.28 2.82 11 7.92 28.96 7.80 2.41 9.78 121.58 1.28 1.51 0.43 1.52 14 8.05 8.33 7.64 2.55 10.60 15 21.39 20.7919.68 7.21 25.70 16 19.78 20.92 19.94 7.72 25.90 17 0.011 0.009 0.0100.003 0.010 18 1207.42 1250.05 1146.04 383.22 1589.91 20 407.20 477.44445.60 167.90 562.29 21 0.15 0.16 0.14 0.05 0.20 13 3.50 5.02 3.16 19345.90 287.73 501.24 Table 116. Provided are the values of each of theparameters (as described above) measured in maize accessions (line)under low nitrogen growth conditions. Growth conditions are specified inthe experimental procedure section.

TABLE 117 Measured parameters in Maize accessions under normal growthconditions Ecotype/Treatment Line-1 Line-2 Line-3 Line-4 Line-5 Line-6 11.27 1.30 1.33 1.50 1.30 1.58 2 19.94 20.17 18.11 19.89 19.50 17.72 316.23 17.50 17.72 18.44 15.67 14.67 4 51.08 46.29 45.92 47.63 51.4147.42 5 11.80 11.11 13.28 11.78 11.94 12.33 6 130.31 122.33 127.67113.02 135.28 94.28 7 273.46 260.50 288.00 238.50 286.94 224.83 8 16.1114.67 15.44 15.89 16.17 15.17 9 56.89 57.16 59.27 61.61 58.63 61.23 1059.93 60.90 56.89 58.70 58.70 63.16 11 2.91 2.64 2.71 2.90 2.70 2.62 128.94 7.02 7.53 7.99 8.48 5.63 14 4.45 3.62 4.01 4.24 4.01 3.12 15 23.4319.05 20.29 20.72 20.49 15.36 16 24.98 17.81 20.33 19.96 19.03 13.90 170.008 0.009 0.009 0.010 0.009 0.011 18 1335.63 1087.06 1202.53 1271.201202.97 937.08 20 456.71 412.44 443.37 438.70 446.66 356.95 21 0.1670.136 0.150 0.159 0.150 0.117 13 3.21 3.95 3.33 4.01 3.86 4.19 19 426.09312.97 307.28 362.44 314.14 224.58 Table 117. Provided are the values ofeach of the parameters (as described above) measured in maize accessions(line) under normal growth conditions. Growth conditions are specifiedin the experimental procedure section.

TABLE 118 Additional measured parameters in Maize accessions undernormal growth conditions Ecotype/Treatment Line-7 Line-8 Line-9 Line-10Line-11 1 1.42 1.37 11.38 1.70 0.42 2 17.67 17.28 20.50 17.50 19.86 312.94 14.03 18.78 12.33 16.07 4 47.25 46.85 49.28 48.28 41.84 5 12.4412.22 12.56 11.67 9.28 6 120.94 107.72 112.50 139.67 60.44 7 264.44251.61 278.44 279.00 163.78 8 16.00 14.83 15.39 17.67 14.27 9 60.1761.09 62.20 57.51 52.04 10 59.75 62.35 61.93 57.23 49.34 11 2.92 2.722.84 2.66 2.26 12 6.10 6.66 8.40 8.21 1.88 14 3.29 3.50 4.55 4.09 1.0015 16.38 17.19 21.96 20.99 5.72 16 16.23 17.21 21.02 21.53 5.52 17 0.0090.009 0.076 0.004 0.003 18 985.89 1050.13 1365.29 1226.08 300.93 20337.49 385.79 481.94 471.57 139.73 21 0.123 0.131 0.171 0.15 0.04 133.97 4.32 2.89 4.31 19 266.44 261.66 482.33 Table 118. Provided are thevalues of each of the parameters (as described above) measured in maizeaccessions (line) under normal growth conditions. Growth conditions arespecified in the experimental procedure section.

TABLE 119 Correlation between the expression level of selected genes ofsome embodiments of the invention in various tissues and the phenotypicperformance under low nitrogen conditions across maize accession GeneExp. Corr. Gene Exp. Corr. Name R P value set Set ID Name R P value setSet ID LGP25 0.93 7.80E−03 1 19 LGP25 0.71 7.10E−02 4 17 LGP25 0.717.10E−02 4 12 LGP27 0.73 6.25E−02 1 18 LGP27 0.73 6.25E−02 1 14 LGP270.75 5.31E−02 1 20 LGP27 0.89 8.05E−03 1 2 LGP27 0.73 6.25E−02 1 21LGP27 0.74 5.58E−02 1 16 LGP27 0.81 4.96E−02 6 10 LGP27 0.81 5.19E−02 63 LGP27 0.72 4.59E−02 8 4 LGP27 0.74 5.64E−02 4 13 LGP27 0.89 6.55E−03 411 LGP72 0.73 2.43E−02 5 4 LGP72 0.85 3.01E−02 6 9 LGP72 0.79 6.10E−02 68 LGP72 0.83 1.15E−02 8 4 LGP72 0.86 6.28E−03 8 5 LGP72 0.86 5.85E−03 86 LGP72 0.78 2.29E−02 7 18 LGP72 0.84 9.09E−03 7 17 LGP72 0.77 2.50E−027 9 LGP72 0.70 5.24E−02 7 4 LGP72 0.87 4.65E−03 7 3 LGP72 0.84 9.82E−037 5 LGP72 0.79 1.94E−02 7 7 LGP72 0.78 2.29E−02 7 14 LGP72 0.75 3.21E−027 20 LGP72 0.78 2.16E−02 7 6 LGP72 0.78 2.11E−02 7 15 LGP72 0.849.09E−03 7 12 LGP72 0.74 3.49E−02 7 1 LGP72 0.78 2.29E−02 7 21 LGP720.75 3.11E−02 7 16 LGP72 0.70 5.24E−02 2 9 LGP72 0.78 3.76E−02 4 5 LGP720.78 3.94E−02 4 1 LGP73 0.88 2.15E−02 6 5 LGP73 0.82 4.77E−02 6 6 LGP730.82 2.40E−02 8 19 LGP73 0.92 3.47E−03 7 13 LGP73 0.93 8.17E−04 7 11LGP73 0.73 6.33E−02 4 9 LGP73 0.72 6.94E−02 4 4 LGP73 0.83 2.20E−02 4 8LGP73 0.80 3.19E−02 4 6 LGP74 0.87 2.35E−02 1 13 LGP74 0.93 6.50E−03 617 LGP74 0.79 6.27E−02 6 4 LGP74 0.73 1.02E−01 6 7 LGP74 0.81 5.11E−02 66 LGP74 0.93 6.50E−03 6 12 LGP74 0.72 4.54E−02 8 7 LGP74 0.80 3.19E−02 819 LGP74 0.98 1.44E−04 2 13 LGP74 0.77 4.50E−02 4 8 LGP75 0.79 3.33E−021 5 LGP75 0.71 7.67E−02 1 1 LGP75 0.71 3.16E−02 5 18 LGP75 0.71 3.16E−025 14 LGP75 0.71 3.16E−02 5 21 LGP75 0.89 1.61E−02 6 18 LGP75 0.824.52E−02 6 4 LGP75 0.74 9.56E−02 6 3 LGP75 0.83 3.91E−02 6 5 LGP75 0.891.61E−02 6 14 LGP75 0.85 3.38E−02 6 6 LGP75 0.96 2.34E−03 6 15 LGP750.88 2.24E−02 6 19 LGP75 0.74 9.43E−02 6 2 LGP75 0.74 9.16E−02 6 1 LGP750.89 1.61E−02 6 21 LGP75 0.89 1.76E−02 6 16 LGP75 0.76 4.85E−02 8 19LGP75 0.74 3.67E−02 7 18 LGP75 0.71 4.78E−02 7 8 LGP75 0.74 3.67E−02 714 LGP75 0.71 4.90E−02 7 20 LGP75 0.73 3.91E−02 7 11 LGP75 0.74 3.67E−027 21 LGP75 0.71 4.73E−02 7 16 LGP75 0.90 2.39E−03 2 17 LGP75 0.772.48E−02 2 5 LGP75 0.90 2.39E−03 2 12 LGP75 0.71 7.62E−02 4 20 LGP750.95 1.12E−03 4 6 LGP75 0.71 7.47E−02 4 2 LGP75 0.78 3.77E−02 4 1 LGP820.88 1.99E−02 1 19 LGP82 0.83 2.06E−02 1 2 LGP82 0.70 7.74E−02 1 1 LGP820.87 2.45E−02 6 5 LGP82 0.80 5.53E−02 6 6 LGP82 0.71 2.14E−02 3 17 LGP820.71 2.14E−02 3 12 LGP82 0.89 7.76E−03 4 17 LGP82 0.78 3.81E−02 4 3LGP82 0.89 7.76E−03 4 12 LGP82 0.72 6.74E−02 4 19 LGP86 0.90 5.23E−03 118 LGP86 0.80 2.93E−02 1 4 LGP86 0.82 2.39E−02 1 3 LGP86 0.87 1.00E−02 15 LGP86 0.90 5.23E−03 1 14 LGP86 0.87 1.03E−02 1 20 LGP86 0.91 4.96E−031 6 LGP86 0.94 1.73E−03 1 15 LGP86 0.76 4.64E−02 1 2 LGP86 0.90 5.23E−031 21 LGP86 0.93 2.57E−03 1 16 LGP86 0.74 1.35E−02 3 18 LGP86 0.721.84E−02 3 10 LGP86 0.74 1.36E−02 3 17 LGP86 0.81 4.17E−03 3 4 LGP860.73 1.55E−02 3 3 LGP86 0.87 1.04E−03 3 5 LGP86 0.74 1.35E−02 3 14 LGP860.92 1.89E−04 3 6 LGP86 0.77 8.94E−03 3 15 LGP86 0.74 1.36E−02 3 12LGP86 0.75 1.29E−02 3 1 LGP86 0.74 1.35E−02 3 21 LGP86 0.76 1.14E−02 316 LGP86 0.88 4.39E−03 8 4 LGP86 0.87 4.51E−03 8 5 LGP86 0.87 5.13E−03 86 LGP86 0.77 2.41E−02 7 18 LGP86 0.71 4.95E−02 7 4 LGP86 0.77 2.41E−02 714 LGP86 0.75 3.29E−02 7 20 LGP86 0.79 2.01E−02 7 15 LGP86 0.79 1.87E−027 2 LGP86 0.77 2.41E−02 7 21 LGP86 0.80 1.63E−02 7 16 LGP86 0.782.33E−02 2 17 LGP86 0.85 7.01E−03 2 5 LGP86 0.74 3.54E−02 2 6 LGP86 0.782.33E−02 2 12 LGP86 0.71 4.72E−02 2 2 LGP86 0.72 6.85E−02 4 10 LGP860.76 4.72E−02 4 3 LGP87 0.83 4.32E−02 1 19 LGP87 0.78 3.89E−02 1 1 LGP870.85 3.24E−02 6 10 LGP87 0.86 2.86E−02 6 4 LGP87 0.78 6.45E−02 6 3 LGP870.76 7.79E−02 6 6 LGP87 0.73 1.56E−02 3 18 LGP87 0.77 8.80E−03 3 10LGP87 0.75 1.18E−02 3 17 LGP87 0.73 1.56E−02 3 9 LGP87 0.91 2.63E−04 3 3LGP87 0.73 1.56E−02 3 14 LGP87 0.76 1.04E−02 3 15 LGP87 0.75 1.18E−02 312 LGP87 0.73 1.56E−02 3 21 LGP87 0.71 2.13E−02 3 16 LGP87 0.70 7.70E−027 13 LGP87 0.78 2.26E−02 7 18 LGP87 0.73 3.81E−02 7 17 LGP87 0.848.72E−03 7 9 LGP87 0.73 4.07E−02 7 3 LGP87 0.91 1.45E−03 7 8 LGP87 0.902.56E−03 7 7 LGP87 0.78 2.26E−02 7 14 LGP87 0.76 2.84E−02 7 20 LGP870.71 5.07E−02 7 15 LGP87 0.73 3.81E−02 7 12 LGP87 0.78 2.26E−02 7 21LGP87 0.73 3.78E−02 7 16 LGP87 0.80 3.02E−02 4 8 LGP88 0.70 7.94E−02 1 8LGP88 0.77 7.19E−02 1 19 LGP88 0.76 2.86E−02 5 19 LGP88 0.71 1.14E−01 68 LGP88 0.71 1.17E−01 6 1 LGP88 0.81 2.79E−02 2 13 LGP88 0.72 4.38E−02 211 LGP88 0.74 5.49E−02 4 18 LGP88 0.74 5.49E−02 4 14 LGP88 0.78 3.69E−024 6 LGP88 0.80 2.95E−02 4 15 LGP88 0.81 2.85E−02 4 19 LGP88 0.783.86E−02 4 2 LGP88 0.92 3.79E−03 4 1 LGP88 0.74 5.49E−02 4 21 LGP88 0.745.50E−02 4 16 LGP89 0.99 3.02E−04 6 18 LGP89 0.76 7.65E−02 6 10 LGP890.83 4.13E−02 6 4 LGP89 0.75 8.65E−02 6 3 LGP89 0.99 3.02E−04 6 14 LGP890.80 5.55E−02 6 20 LGP89 0.96 2.89E−03 6 15 LGP89 0.86 2.90E−02 6 19LGP89 0.80 5.50E−02 6 2 LGP89 0.99 3.02E−04 6 21 LGP89 0.96 2.69E−03 616 LGP89 0.84 9.63E−03 2 2 LGP89 0.77 4.23E−02 4 9 LGP89 0.91 4.56E−03 48 LGP90 0.76 4.92E−02 1 5 LGP90 0.73 6.36E−02 1 6 LGP90 0.73 9.83E−02 65 LGP90 0.80 5.80E−02 6 6 LGP90 0.71 7.56E−02 8 19 LGP90 0.77 2.56E−02 217 LGP90 0.72 4.41E−02 2 5 LGP90 0.77 2.56E−02 2 12 LGP90 0.80 3.10E−024 9 LGP91 0.83 3.87E−02 6 18 LGP91 0.83 3.87E−02 6 14 LGP91 0.786.64E−02 6 20 LGP91 0.75 8.53E−02 6 15 LGP91 0.77 7.25E−02 6 19 LGP910.76 7.95E−02 6 2 LGP91 0.74 9.26E−02 6 1 LGP91 0.83 3.87E−02 6 21 LGP910.80 5.45E−02 6 16 LGP91 0.85 7.35E−03 8 8 LGP91 0.88 8.62E−03 7 13LGP91 0.97 8.43E−05 7 11 LGP92 0.93 7.17E−03 1 13 LGP92 0.70 7.72E−02 19 LGP92 0.71 7.41E−02 1 8 LGP92 0.86 1.34E−02 1 11 LGP92 0.70 7.78E−02 11 LGP92 0.71 4.87E−02 5 19 LGP92 0.79 6.19E−02 6 5 LGP92 0.88 1.99E−02 66 LGP92 0.73 1.72E−02 3 1 LGP92 0.82 1.28E−02 8 7 LGP92 0.90 6.33E−03 713 LGP92 0.84 9.32E−03 7 11 LGP92 0.94 1.41E−03 2 13 LGP92 0.77 4.34E−024 8 LGP94 0.81 1.57E−02 5 13 LGP94 0.93 6.59E−03 6 13 LGP94 0.853.09E−02 6 11 LGP94 0.72 2.81E−02 3 13 LGP94 0.94 1.68E−03 8 13 LGP940.82 1.36E−02 8 11 LGP94 0.89 7.44E−03 7 13 LGP94 0.86 5.67E−03 7 11LGP94 0.80 3.08E−02 2 13 LGP94 0.78 2.15E−02 2 17 LGP94 0.71 5.03E−02 25 LGP94 0.79 1.94E−02 2 11 LGP94 0.78 2.15E−02 2 12 LGP94 0.84 1.91E−024 13 LGP94 0.94 1.38E−03 4 11 LGP95 0.92 3.68E−03 1 10 LGP95 0.783.89E−02 1 9 LGP95 0.72 6.80E−02 1 7 LGP95 0.79 5.94E−02 6 13 LGP95 0.788.28E−03 3 18 LGP95 0.82 3.49E−03 3 17 LGP95 0.82 3.51E−03 3 9 LGP950.73 1.65E−02 3 3 LGP95 0.78 8.28E−03 3 14 LGP95 0.75 1.19E−02 3 20LGP95 0.75 1.27E−02 3 15 LGP95 0.82 3.49E−03 3 12 LGP95 0.78 8.28E−03 321 LGP95 0.74 1.44E−02 3 16 LGP95 0.75 3.27E−02 8 20 LGP95 0.79 3.44E−022 13 Table 119. Correlations (R) between the genes expression levels invarious tissues and the phenotypic performance under low nitrogenconditions. “Corr. ID “—correlation set ID according to the correlatedparameters Table above. “Exp. Set”—Expression set. “R” = Pearsoncorrelation coefficient; “P” = p value.

TABLE 120 Correlation between the expression level of selected genes ofsome embodiments of the invention in various tissues and the phenotypicperformance under normal conditions across maize accessions Gene Exp.Corr. Gene Corr. Name R P value set Set ID Name R P value Exp. set SetID LGP25 0.80 5.67E−02 5 5 LGP27 0.75 3.10E−02 2 4 LGP27 0.71 7.37E−02 410 LGP27 0.84 1.71E−02 6 5 LGP27 0.73 6.35E−02 6 6 LGP27 0.75 5.26E−02 68 LGP72 0.76 7.91E−02 5 4 LGP72 0.83 1.00E−02 2 4 LGP72 0.70 5.29E−02 26 LGP72 0.77 4.49E−02 4 8 LGP72 0.75 3.13E−02 3 17 LGP72 0.70 5.10E−02 34 LGP72 0.73 3.78E−02 3 10 LGP72 0.75 3.13E−02 3 1 LGP72 0.73 6.48E−02 65 LGP72 0.73 6.38E−02 6 4 LGP72 0.77 4.15E−02 6 8 LGP72 0.84 5.00E−03 717 LGP72 0.84 5.00E−03 7 1 LGP73 0.91 1.10E−02 5 5 LGP73 0.72 6.81E−02 69 LGP74 0.79 5.98E−02 1 13 LGP74 0.74 3.76E−02 7 13 LGP75 0.91 4.31E−031 7 LGP75 0.90 5.66E−03 1 12 LGP75 0.80 2.98E−02 1 11 LGP75 0.861.29E−02 1 5 LGP75 0.92 3.14E−03 1 15 LGP75 0.91 3.97E−03 1 14 LGP750.83 2.13E−02 1 4 LGP75 0.90 5.76E−03 1 16 LGP75 0.87 1.11E−02 1 6 LGP750.91 3.97E−03 1 18 LGP75 0.72 7.03E−02 1 8 LGP75 0.91 3.97E−03 1 21LGP75 0.75 5.11E−02 1 9 LGP75 0.94 1.89E−03 1 20 LGP75 0.87 2.37E−02 512 LGP75 0.74 9.57E−02 5 17 LGP75 0.81 4.83E−02 5 11 LGP75 0.84 3.46E−025 15 LGP75 0.90 1.41E−02 5 14 LGP75 0.79 6.06E−02 5 4 LGP75 0.767.65E−02 5 16 LGP75 0.90 1.41E−02 5 18 LGP75 0.95 3.57E−03 5 8 LGP750.90 1.41E−02 5 21 LGP75 0.74 9.57E−02 5 1 LGP75 0.97 1.57E−03 5 19LGP75 0.85 3.29E−02 5 20 LGP75 0.94 4.77E−03 5 2 LGP75 0.74 1.36E−02 812 LGP75 0.76 1.09E−02 8 15 LGP75 0.76 1.11E−02 8 14 LGP75 0.76 1.01E−028 16 LGP75 0.76 1.11E−02 8 18 LGP75 0.76 1.11E−02 8 21 LGP75 0.741.54E−02 8 20 LGP75 0.93 9.88E−04 3 3 LGP75 0.74 3.62E−02 3 20 LGP750.71 3.09E−02 7 7 LGP75 0.73 2.52E−02 7 12 LGP75 0.79 1.06E−02 7 15LGP75 0.78 1.38E−02 7 14 LGP75 0.75 1.93E−02 7 16 LGP75 0.78 1.38E−02 718 LGP75 0.78 1.38E−02 7 21 LGP75 0.79 1.05E−02 7 20 LGP80 0.97 1.07E−035 5 LGP82 0.73 2.65E−02 7 7 LGP82 0.83 5.88E−03 7 6 LGP86 0.79 3.59E−021 7 LGP86 0.94 1.60E−03 1 5 LGP86 0.70 7.81E−02 1 15 LGP86 0.71 7.61E−021 14 LGP86 0.74 5.79E−02 1 16 LGP86 0.74 5.72E−02 1 6 LGP86 0.717.61E−02 1 18 LGP86 0.70 7.88E−02 1 8 LGP86 0.71 7.61E−02 1 21 LGP860.72 6.62E−02 1 20 LGP86 0.73 9.84E−02 5 4 LGP86 0.80 3.03E−02 4 7 LGP860.91 4.35E−03 4 12 LGP86 0.84 1.73E−02 4 11 LGP86 0.92 3.24E−03 4 15LGP86 0.90 5.84E−03 4 14 LGP86 0.71 7.44E−02 4 4 LGP86 0.91 4.82E−03 416 LGP86 0.78 3.86E−02 4 3 LGP86 0.87 1.19E−02 4 6 LGP86 0.90 5.84E−03 418 LGP86 0.73 6.27E−02 4 8 LGP86 0.90 5.84E−03 4 21 LGP86 0.78 6.87E−024 19 LGP86 0.89 6.97E−03 4 20 LGP86 0.70 7.88E−02 6 7 LGP86 0.764.55E−02 6 12 LGP86 0.71 7.23E−02 6 11 LGP86 0.79 3.57E−02 6 15 LGP860.76 4.62E−02 6 14 LGP86 0.78 3.74E−02 6 16 LGP86 0.82 2.54E−02 6 6LGP86 0.76 4.62E−02 6 18 LGP86 0.82 2.35E−02 6 8 LGP86 0.76 4.62E−02 621 LGP86 0.77 4.40E−02 6 20 LGP86 0.75 1.95E−02 7 12 LGP86 0.71 3.22E−027 11 LGP86 0.78 1.25E−02 7 15 LGP86 0.73 2.61E−02 7 14 LGP86 0.844.57E−03 7 16 LGP86 0.79 1.17E−02 7 6 LGP86 0.73 2.61E−02 7 18 LGP860.73 2.61E−02 7 21 LGP87 0.71 1.14E−01 5 5 LGP87 0.81 1.59E−02 2 10LGP87 0.78 6.88E−02 6 13 LGP87 0.75 2.06E−02 7 4 LGP87 0.71 3.25E−02 7 8LGP88 0.86 2.67E−02 1 13 LGP88 0.70 1.18E−01 5 17 LGP88 0.70 1.18E−01 51 LGP88 0.73 2.50E−02 8 13 LGP89 0.87 2.60E−02 5 5 LGP89 0.90 2.15E−03 217 LGP89 0.90 2.15E−03 2 1 LGP89 0.70 7.69E−02 6 3 LGP89 0.86 1.26E−02 68 LGP89 0.70 5.16E−02 7 13 LGP90 0.85 1.51E−02 1 7 LGP90 0.81 2.75E−02 112 LGP90 0.83 2.19E−02 1 15 LGP90 0.78 3.87E−02 1 14 LGP90 0.82 2.42E−021 16 LGP90 0.94 1.58E−03 1 6 LGP90 0.78 3.87E−02 1 18 LGP90 0.783.87E−02 1 21 LGP90 0.82 2.33E−02 1 20 LGP90 0.86 2.90E−02 5 8 LGP900.75 3.15E−02 2 5 LGP91 0.81 2.82E−02 1 3 LGP91 0.70 1.18E−01 5 3 LGP910.72 1.83E−02 8 5 LGP91 0.76 1.02E−02 8 9 LGP91 0.72 6.95E−02 4 7 LGP910.75 5.46E−02 4 12 LGP91 0.78 3.80E−02 4 15 LGP91 0.73 6.09E−02 4 14LGP91 0.74 5.74E−02 4 16 LGP91 0.84 1.79E−02 4 6 LGP91 0.73 6.09E−02 418 LGP91 0.73 6.09E−02 4 21 LGP91 0.77 4.41E−02 4 20 LGP91 0.73 3.85E−023 2 LGP92 0.74 5.88E−02 1 7 LGP92 0.72 6.69E−02 1 5 LGP92 0.71 7.48E−021 10 LGP92 0.77 7.18E−02 5 8 LGP92 0.85 3.36E−02 6 13 LGP92 0.826.75E−03 7 4 LGP94 0.84 3.69E−02 5 10 LGP94 0.70 7.89E−02 4 12 LGP940.72 6.91E−02 4 15 LGP94 0.78 3.68E−02 4 6 LGP94 0.80 3.25E−02 6 7 LGP940.86 1.41E−02 6 5 LGP95 0.87 2.32E−02 5 5 LGP95 0.74 3.72E−02 2 17 LGP950.74 3.72E−02 2 1 LGP95 0.71 2.24E−02 8 12 LGP95 0.76 2.78E−02 3 5 Table120. Correlations (R) between the genes expression levels in varioustissues and the phenotypic performance under low nitrogen conditions.“Corr. ID “—correlation set ID according to the correlated parametersTable above. “Exp. Set”—Expression set. “R” = Pearson correlationcoefficient; “P” = p value.

Example 15 Production of Brachypodium Transcriptome and High ThroughputCorrelation Analysis Using 60K Brachypodium Oligonucleotide Micro-Array

In order to produce a high throughput correlation analysis comparingbetween plant phenotype and gene expression level, the present inventorsutilized a brachypodium oligonucleotide micro-array, produced by AgilentTechnologies [chem. (dot) agilent (dot) com/Scripts/PDS (dot)asp?1Page=50879]. The array oligonucleotide represents about 60Kbrachypodium genes and transcripts. In order to define correlationsbetween the levels of RNA expression and yield or vigor relatedparameters, various plant characteristics of 24 different brachypodiumaccessions were analyzed. Among them, 22 accessions encompassing theobserved variance were selected for RNA expression analysis andcomparative genomic hybridization (CGH) analysis.

The correlation between the RNA levels and the characterized parameterswas analyzed using Pearson correlation test [davidmlane (dot)com/hyperstat/A34739 (dot) html].

Additional correlation analysis was done by comparing plant phenotypeand gene copy number. The correlation between the normalized copy numberhybridization signal and the characterized parameters was analyzed usingPearson correlation test [davidmlane (dot) com/hyperstat/A34739 (dot)html].

Experimental Procedures

Analyzed Brachypodium tissues—two tissues [leaf and spike] were sampledand RNA was extracted as described above. Each micro-array expressioninformation tissue type has received a Set ID as summarized in Table 121below.

TABLE 121 Brachypodium transcriptome expression sets Expression Set SetID Leaf at flowering stage under normal growth conditions 1 Spike atflowering stage under normal growth conditions 2 Leaf at flowering stageunder normal growth conditions 3 Table 121. From set ID No. 3 the samplewas used to extract DNA; from set ID Nos. 1 and 2 the samples were usedto extract RNA.

Brachypodium Yield Components and Vigor Related Parameters Assessment—

24 brachypodium accessions were grown in 4-6 repetitive plots (8 plantsper plot) in a green house. The growing protocol was as follows:brachypodium seeds were sown in plots and grown under normal condition(6 mM of Nitrogen as ammonium nitrate) or reduced N level (low N, 35% ofnormal nitrogen fertilization). Plants were continuously phenotypedduring the growth period and at harvest (Table 123-124, below). Theimage analysis system include d a personal desktop computer (Intel P43.0 GHz processor) and a public domain program—ImageJ 1.37 (Java basedimage processing program, which was developed at the U.S. NationalInstitutes of Health and freely available on the internet [rsbweb (dot)nih (dot) gov/]. Next, analyzed data was saved to text files andprocessed using the JMP statistical analysis software (SAS institute).

At the end of the growing period the grains were separated from thespikes and the following parameters were measured using digital imagingsystem and collected:

Number of tillering—all tillers were counted per plant at harvest (meanper plot).

Head number—At the end of the experiment, heads were harvested from eachplot and were counted.

Total Grains weight per plot (gr.)—At the end of the experiment (plant‘Heads’) heads from plots were collected, the heads were threshed andgrains were weighted. In addition, the average grain weight per head wascalculated by dividing the total grain weight by number of total headsper plot (based on plot).

Highest number of spikelets—The highest spikelet number per head wascalculated per plant (mean per plot).

Mean number of spikelets—The mean spikelet number per head wascalculated per plot.

Plant height—Each of the plants was measured for its height usingmeasuring tape. Height was measured from ground level to spike base ofthe longest spike at harvest.

Vegetative dry weight and spike yield—At the end of the experiment (50%of the spikes were dry) all spikes and vegetative material from plotswere collected. The biomass and spikes weight of each plot wasseparated, measured and divided by the number of plants/plots.

Dry weight—total weight of the vegetative portion above ground(excluding roots) after drying at 70° C. in oven for 48 hours;

Spike yield per plant=total spike weight per plant (gr) after drying at30° C. in oven for 48 hours. Spikelets weight (gr.)—The biomass andspikes weight of each plot was separated and measured per plot.

Average head weight—calculated by dividing spikelets weight with headnumber (gr.).

Harvest Index—The harvest index was calculated using Formula XV(described above).

Spikelets Index—The Spikelets index is calculated using Formula XXXIabove.

Percent Number of heads with spikelets—The number of heads with morethan one spikelet per plant were counted and the percent from all headsper plant was calculated.

Total dry mater per plot—Calculated as Vegetative portion above groundplus all the spikelet dry weight per plot.

1000 grain weight—At the end of the experiment all grains from all plotswere collected and weighted and the weight of 1000 grains wascalculated.

The following parameters were collected using digital imaging system: Atthe end of the growing period the grains were separated from the spikesand the following parameters were measured and collected:

(i) Average Grain Area (cm²)—A sample of ˜200 grains was weighted,photographed and images were processed using the below described imageprocessing system. The grain area was measured from those images and wasdivided by the number of grains.

(ii) Average Grain Length, perimeter and width (cm)—A sample of ˜200grains was weighted, photographed and images were processed using thebelow described image processing system. The sum of grain lengths andwidth (longest axis) was measured from those images and was divided bythe number of grains.

The image processing system was used, which consists of a personaldesktop computer (Intel P4 3.0 GHz processor) and a public domainprogram—ImageJ 1.37,

Java based image processing software, which was developed at the U.S.National Institutes of Health and is freely available on the internet atrsbweb (dot) nih (dot) gov/. Images were captured in resolution of 10Mega Pixels (3888×2592 pixels) and stored in a low compression JPEG(Joint Photographic Experts Group standard) format. Next, imageprocessing output data for seed area and seed length was saved to textfiles and analyzed using the JMP statistical analysis software (SASinstitute).

TABLE 122 Brachypodium correlated parameters (vectors) Correlatedparameter with Correlation ID % Number of heads with spikelets (%) 11000 grain weight (gr.) 2 Average head weight (gr.) 3 Grain area (cm²) 5Grain length (cm) 6 Grain Perimeter (cm) 4 Grain width (cm) 7 Grainsweight per plant (gr.) 8 Grains weight per plot (gr.) 9 Harvest index 10Heads per plant 11 Heads per plot 12 Highest number of spikelets perplot 13 Mean number of spikelets per plot 14 Number of heads withspikelets per plant 15 Plant height (cm) 17 Plant Vegetative DW (gr.) 16Plants number 18 Spikelets DW per plant (gr.) 19 Spikelets weight (gr.)20 Spikes index 21 Tittering (number) 22 Total dry mater per plant (gr.)23 Total dry mater per plot (gr.) 24 Vegetative DW (gr.) 25 Table 122.Provided are the Brachypodium correlated parameters. Correlation IDs1-21 are identical to correlation IDs 26-46, respectively, andcorrelation IDs 23-25 are identical to correlation IDs 47-49,respectively.

Experimental Results

24 different Brachypodium accessions were grown and characterized fordifferent parameters as described above. The average for each of themeasured parameter was calculated using the JMP software and values aresummarized in Tables 123-125 below. Subsequent correlation analysisbetween the various transcriptome sets and the average parameters (Table126) was conducted. Follow, results were integrated to the database.

TABLE 123 Measured parameters of correlation IDs in Brachypodiumaccessions under normal conditions Ecotype/Treatment Line-1 Line-2Line-3 Line-4 Line-5 Line-6 Line-7 Line-8 1 27.61 35.33 21.67 52.4020.84 47.73 17.55 16.51 2 3.75 3.78 3.35 3.70 3.90 4.87 4.82 4.76 3 0.060.04 0.05 0.09 0.04 0.09 0.06 0.06 4 1.67 1.62 1.62 1.65 1.60 1.90 1.801.82 5 0.10 0.10 0.09 0.09 0.09 0.11 0.10 0.11 6 0.73 0.72 0.72 0.750.72 0.87 0.79 0.79 7 0.18 0.17 0.17 0.15 0.15 0.16 0.17 0.18 8 0.140.06 0.08 0.35 0.27 0.44 0.32 0.07 9 1.05 0.44 0.61 2.58 2.03 3.40 2.580.39 10 0.13 0.14 0.15 0.21 0.17 0.18 0.15 0.11 11 16.29 7.08 6.59 16.1121.40 17.05 25.88 8.02 12 121.75 56.60 52.75 123.50 156.83 135.00 207.0048.60 13 3.00 2.60 3.00 2.83 2.33 4.50 2.60 2.00 14 2.10 2.10 1.72 2.171.85 2.85 1.93 1.56 15 5.27 2.50 2.06 9.44 5.02 7.72 4.90 1.87 16 0.420.12 0.13 0.82 0.67 1.05 0.87 0.31 17 31.65 23.44 22.75 45.35 29.4146.74 38.39 29.15 18 7.50 8.00 8.00 7.50 7.33 7.88 8.00 6.40 19 0.960.31 0.33 1.46 0.96 1.42 1.56 0.45 20 7.18 2.50 2.68 11.31 7.16 11.0512.44 2.66 21 0.71 0.72 0.73 0.68 0.60 0.57 0.65 0.60 22 16.84 7.20 7.0016.99 23.61 18.25 27.20 8.60 23 1.38 0.43 0.47 2.28 1.63 2.47 2.43 0.7624 10.26 3.45 3.74 17.78 12.29 19.27 19.40 4.47 25 3.08 0.95 1.06 6.475.13 8.23 6.96 1.81 Table 123. Correlation IDs: 1, 2, 3, 4, 5, . . .etc. refer to those described in Table 122 above [Brachypodiumcorrelated parameters (vectors)].

TABLE 124 Measured parameters of correlation IDs in brachypodiumaccessions under normal conditions Ecotype/Treatment Line-9 Line-10Line-11 Line-12 Line-13 Line-14 Line-15 1 5.42 15.42 14.00 6.40 4.5115.52 20.34 2 5.54 4.98 4.88 4.83 5.54 4.73 5.24 3 0.04 0.06 0.07 0.050.04 0.05 0.05 4 1.82 1.83 1.69 1.74 1.93 1.69 1.91 5 0.11 0.11 0.090.10 0.11 0.10 0.12 6 0.83 0.82 0.74 0.78 0.90 0.75 0.86 7 0.16 0.170.16 0.17 0.16 0.17 0.19 8 0.14 0.14 0.26 0.14 0.11 0.39 0.14 9 1.111.07 1.96 1.09 0.84 3.07 1.09 10 0.20 0.16 0.20 0.14 0.26 0.22 0.09 1110.48 9.09 11.63 14.13 5.88 23.75 16.06 12 82.40 70.13 83.40 110.3347.00 185.50 125.00 13 2.00 2.25 2.20 1.83 2.00 2.50 2.40 14 1.38 1.651.69 1.43 1.25 1.76 1.83 15 0.71 1.94 2.08 1.08 0.35 4.98 3.70 16 0.320.32 0.38 0.39 0.13 0.87 0.69 17 34.36 28.65 31.95 28.88 24.74 37.3045.09 18 7.80 7.75 7.20 7.83 8.00 7.75 8.00 19 0.44 0.56 0.88 0.67 0.261.14 0.83 20 3.45 4.29 6.42 5.29 2.04 8.89 6.65 21 0.58 0.66 0.71 0.640.66 0.59 0.54 22 10.67 9.38 11.97 14.58 6.35 25.50 16.56 23 0.76 0.881.25 1.06 0.38 2.01 1.53 24 6.00 6.78 9.12 8.34 3.04 15.79 12.20 25 2.552.48 2.69 3.05 1.00 6.89 5.55 Table 124. Correlation IDs: 1, 2, 3, 4, 5,. . . etc. refer to those described in Table 15.2 above [Brachypodiumcorrelated parameters (vectors)].

TABLE 125 Measured parameters of correlation IDs in brachypodiumaccessions under normal conditions Ecotype/Treatment Line-16 Line-17Line-18 Line-19 Line-20 Line-21 Line-22 1 8.11 53.21 55.41 47.81 42.8159.01 34.92 2 4.96 4.00 3.84 4.26 5.99 3.76 4.34 3 0.06 0.10 0.08 0.080.08 0.09 0.06 4 1.71 1.81 1.68 1.75 1.87 1.68 1.66 5 0.10 0.10 0.100.09 0.12 0.09 0.09 6 0.74 0.84 0.75 0.80 0.84 0.76 0.74 7 0.17 0.150.17 0.14 0.18 0.15 0.16 8 0.13 0.37 0.08 0.49 0.31 0.30 0.20 9 1.072.99 0.50 3.52 2.41 1.92 1.47 10 0.18 0.09 0.07 0.16 0.18 0.09 0.11 119.74 22.19 11.89 24.32 13.25 25.54 19.22 12 80.75 177.50 81.50 172.8098.60 177.00 143.17 13 2.00 3.50 3.50 3.80 2.80 3.17 2.83 14 1.42 2.712.41 2.61 2.12 2.79 2.15 15 0.89 12.58 7.59 12.13 6.35 15.36 7.15 160.34 1.72 0.44 1.32 0.48 1.73 0.63 17 22.39 55.04 31.40 45.34 40.2058.82 39.18 18 8.25 8.00 6.50 7.00 7.60 6.83 7.33 19 0.59 2.27 0.92 1.911.09 2.25 1.26 20 4.92 18.15 6.25 13.49 8.35 15.55 9.42 21 0.68 0.560.69 0.59 0.70 0.57 0.66 22 10.53 27.15 12.38 26.30 13.56 29.09 20.79 230.93 3.99 1.36 3.23 1.57 3.98 1.89 24 7.76 31.94 9.21 22.78 12.04 27.6714.14 25 2.84 13.80 2.96 9.28 3.70 12.12 4.72 Table 125. CorrelationIDs: 1, 2, 3, 4, 5, . . . etc. refer to those described in Table 122above [Brachypodium correlated parameters (vectors)].

TABLE 126 Correlation between the expression level of selected genes ofsome embodiments of the invention in various tissues and the phenotypicperformance under normal conditions across brachypodium varieties GeneName R P value Exp. set Correl. Set ID MGP6 0.72 8.12E−03 3 2 Table 126.Provided are the correlations (R) between the expression levels yieldimproving genes and their homologs in various tissues [Expression (Exp)sets] and the phenotypic performance [yield, biomass, growth rate and/orvigor components (Correlation vector (Corr.))] under normal conditionsacross brachypodium varieties. P = p value.

Example 16 Production of Soybean (Glycine Max) Transcriptome and HighThroughput Correlation Analysis with Yield Parameters Using 44K B.Soybean Oligonucleotide Micro-Arrays

In order to produce a high throughput correlation analysis, the presentinventors utilized a Soybean oligonucleotide micro-array, produced byAgilent Technologies [chem. (dot) agilent (dot) com/Scripts/PDS (dot)asp?1Page=50879]. The array oligonucleotide represents about 42,000Soybean genes and transcripts. In order to define correlations betweenthe levels of RNA expression with yield components or plant architecturerelated parameters or plant vigor related parameters, various plantcharacteristics of 29 different Glycine max varieties were analyzed and26 varieties were further used for RNA expression analysis. Thecorrelation between the RNA levels and the characterized parameters wasanalyzed using Pearson correlation test.

Correlation of Glycine max Genes' Expression Levels with PhenotypicCharacteristics Across Ecotype

Experimental Procedures

29 Soybean varieties were grown in three repetitive plots in field.Briefly, the growing protocol was as follows: Soybean seeds were sown insoil and grown under normal conditions (no irrigation, good organomicparticles) which included high temperature about 82.38 (° F.), lowtemperature about 58.54 (° F.); total precipitation rainfall from Maythrough September (from sowing until harvest) was about 16.97 inch.

In order to define correlations between the levels of RNA expressionwith yield components or plant architecture related parameters or vigorrelated parameters, 26 different Soybean varieties (out of 29 varieties)were analyzed and used for gene expression analyses. Analysis wasperformed at two pre-determined time periods: at pod set (when thesoybean pods are formed) and at harvest time (when the soybean pods areready for harvest, with mature seeds).

TABLE 127 Soybean transcriptome expression sets Expression Set Set IDApical meristem at vegetative stage under normal growth 1 condition Leafat vegetative stage under normal growth condition 2 Leaf at floweringstage under normal growth condition 3 Leaf at pod setting stage undernormal growth condition 4 Root at vegetative stage under normal growthcondition 5 Root at flowering stage under normal growth condition 6 Rootat pod setting stage under normal growth condition 7 Stem at vegetativestage under normal growth condition 8 Stem at pod setting stage undernormal growth condition 9 Flower bud at flowering stage under normalgrowth condition 10 Pod (R3-R4) at pod setting stage under normal growthcondition 11 Table 127.

RNA extraction—All 12 selected Soybean varieties were sample pertreatment. Plant tissues [leaf, root, Stem, Pod, apical meristem, Flowerbuds] growing under normal conditions were sampled and RNA was extractedas described above. The collected data parameters were as follows:

Main branch base diameter [mm] at pod set—the diameter of the base ofthe main branch (based diameter) average of three plants per plot.

Fresh weight [gr./plant] at pod set]—total weight of the vegetativeportion above ground (excluding roots) before drying at pod set, averageof three plants per plot.

Dry weight [gr./plant] at pod set—total weight of the vegetative portionabove ground (excluding roots) after drying at 70° C. in oven for 48hours at pod set, average of three plants per plot.

Total number of nodes with pods on lateral branches[value/plant]—counting of nodes which contain pods in lateral branchesat pod set, average of three plants per plot.

Number of lateral branches at pod set [value/plant]—counting number oflateral branches at pod set, average of three plants per plot.

Total weight of lateral branches at pod set [gr./plant]—weight of alllateral branches at pod set, average of three plants per plot.

Total weight of pods on main stem at pod set [gr./plant]—weight of allpods on main stem at pod set, average of three plants per plot.

Total number of nodes on main stem [value/plant]—count of number ofnodes on main stem starting from first node above ground, average ofthree plants per plot.

Total number of pods with 1 seed on lateral branches at pod set[value/plant]—count of the number of pods containing 1 seed in alllateral branches at pod set, average of three plants per plot.

Total number of pods with 2 seeds on lateral branches at pod set[value/plant]—count of the number of pods containing 2 seeds in alllateral branches at pod set, average of three plants per plot.

Total number of pods with 3 seeds on lateral branches at pod set[value/plant]—count of the number of pods containing 3 seeds in alllateral branches at pod set, average of three plants per plot.

Total number of pods with 4 seeds on lateral branches at pod set[value/plant]—count of the number of pods containing 4 seeds in alllateral branches at pod set, average of three plants per plot.

Total number of pods with 1 seed on main stem at pod set[value/plant]—count of the number of pods containing 1 seed in main stemat pod set, average of three plants per plot.

Total number of pods with 2 seeds on main stem at pod set[value/plant]—count of the number of pods containing 2 seeds in mainstem at pod set, average of three plants per plot.

Total number of pods with 3 seeds on main stem at pod set[value/plant]—count of the number of pods containing 3 seeds in mainstem at pod set, average of three plants per plot.

Total number of pods with 4 seeds on main stem at pod set[value/plant]—count of the number of pods containing 4 seeds in mainstem at pod set, average of three plants per plot.

Total number of seeds per plant at pod set [value/plant]—count of numberof seeds in lateral branches and main stem at pod set, average of threeplants per plot.

Total number of seeds on lateral branches at pod set [value/plant]—countof total number of seeds on lateral branches at pod set, average ofthree plants per plot.

Total number of seeds on main stem at pod set [value/plant]—count oftotal number of seeds on main stem at pod set, average of three plantsper plot.

Plant height at pod set [cm/plant]—total length from above ground tillthe tip of the main stem at pod set, average of three plants per plot.

Plant height at harvest [cm/plant]—total length from above ground tillthe tip of the main stem at harvest, average of three plants per plot.

Total weight of pods on lateral branches at pod set [gr./plant]—weightof all pods on lateral branches at pod set, average of three plants perplot.

Ratio of the number of pods per node on main stem at pod set—calculatedin Formula XXIII (above), average of three plants per plot.

Ratio of total number of seeds in main stem to number of seeds onlateral branches—calculated in Formula XXIV above, average of threeplants per plot.

Total weight of pods per plant at pod set [gr./plant]—weight of all podson lateral branches and main stem at pod set, average of three plantsper plot.

Days till 50% flowering [days]—number of days till 50% flowering foreach plot.

Days till 100% flowering [days]—number of days till 100% flowering foreach plot.

Maturity [days]—measure as 95% of the pods in a plot have ripened(turned 100% brown). Delayed leaf drop and green stems are notconsidered in assigning maturity. Tests are observed 3 days per week,every other day, for maturity. The maturity date is the date that 95% ofthe pods have reached final color. Maturity is expressed in days afterAugust 31 [according to the accepted definition of maturity in USA,Descriptor list for SOYBEAN, ars-grin (dot)gov/cgi-bin/npgs/html/desclist (dot) pl?51].

Seed quality [ranked 1-5]—measure at harvest; a visual estimate based onseveral hundred seeds. Parameter is rated according to the followingscores considering the amount and degree of wrinkling, defective coat(cracks), greenishness, and moldy or other pigment. Rating is “1”—verygood, “2”—good, “3”—fair, “4”—poor, “5”—very poor.

Lodging [ranked 1-5]—is rated at maturity per plot according to thefollowing scores: “1”—most plants in a plot are erected; “2”—all plantsleaning slightly or a few plants down; “3”—all plants leaningmoderately, or 25%-50% down; “4”—all plants leaning considerably, or50%-80% down; “5”—most plants down. Note: intermediate score such as 1.5are acceptable.

Seed size [gr.]—weight of 1000 seeds per plot normalized to 13%moisture, measure at harvest.

Total weight of seeds per plant [gr./plant]—calculated at harvest (per 2inner rows of a trimmed plot) as weight in grams of cleaned seedsadjusted to 13% moisture and divided by the total number of plants intwo inner rows of a trimmed plot.

Yield at harvest [bushels/hectare]—calculated at harvest (per 2 innerrows of a trimmed plot) as weight in grams of cleaned seeds, adjusted to13% moisture, and then expressed as bushels per acre.

Average lateral branch seeds per pod [number]—Calculate number of seedson lateral branches-at pod set and divide by the number of pods withseeds on lateral branches-at pod set.

Average main stem seeds per pod [number]—Calculate total number of seedson main stem at pod set and divide by the number of pods with seeds onmain stem at pod setting.

Main stem average internode length [cm]—Calculate plant height at podset and divide by the total number of nodes on main stem at pod setting.

Total number of pods with seeds on main stem [number]—count all podscontaining seeds on the main stem at pod setting.

Total number of pods with seeds on lateral branches [number]—count allpods containing seeds on the lateral branches at pod setting.

Total number of pods per plant at pod set [number]—count pods on mainstem and lateral branches at pod setting.

TABLE 128 Soybean correlated parameters (vectors) Correlation Correlatedparameter with ID 100 percent flowering (days) 1 50 percent flowering(days) 2 Base diameter at pod set (mm) 3 DW at pod set (gr) 4 Lodging(score 1-5) 5 Maturity (days) 6 Num of lateral branches (number) 7 Numof pods with 1 seed on main stem at pod set (number) 8 Num of pods with2 seed on main stem at pod set (number) 9 Num of pods with 3 seed onmain stem at pod set (number) 10 Num of pods with 4 seed on main stem atpod set (number) 11 Plant height at harvest (cm) 12 Plant height at podset (cm) 13 Ratio number of pods per node on main stem (ratio) 14 Rationum of seeds-main stem to lateral branches (ratio) 15 Seed quality(score 1-5) 16 1000 seed weight (gr) 17 Num of Seeds on lateralbranches-at pod set 18 Total Number of Seeds on main stem at pod set(number) 19 Num of pods with 1 seed on lateral branch-pod set 20(number) Num of pods with 2 seed on lateral branch-pod set 21 (number)Num pods with 3 seed on lateral branch-at pod set (number) 22 Num podswith 4 seed on lateral branch-at pod set (number) 23 Total number ofnodes on main stem (number) 24 Num of nodes with pods on lateralbranches-pod set 25 (number) Total number of seeds per plant (number) 26Total weight of lateral branches at pod set (gr) 27 Weight of pods onlateral branches (gr)-at pod set 28 Total weight of pods on main stem atpod set (gt) 29 Total weight of pods per plant (gr/plant) 30 Totalweight of seeds per plant (gr/plant) 31 fresh weight at pod set (gr) 32yield at harvest (bushel/hectare) 33 Average lateral branch seeds perpod 34 Average main stem seeds per pod 35 Main stem average internodelength 36 Num pods with seeds on lateral branches-at pod set 37 (number)Total number of pods per plant (number) 38 Total number of pods withseeds on main stem (number) 39 corrected Seed size (gr) 40 Table 128.

Experimental Results

29 different Soybean varieties lines were grown and characterized for 40parameters as specified above. Tissues for expression analysis weresampled from a subset of 12 lines. The correlated parameters aredescribed in Table 128 above. The average for each of the measuredparameter was calculated using the JMP software (Tables 129-134) and asubsequent correlation analysis was performed (Tables 135-136). Resultswere then integrated to the database.

TABLE 129 Measured parameters in Soybean varieties (lines 1-6) Ecotype/Treatment Line-1 Line-2 Line-3 Line-4 Line-5 Line-6 1 67.33 71.67 67.6767.33 60.00 74.00 2 61.00 65.33 60.67 61.00 54.67 68.33 3 8.33 9.54 9.688.11 8.82 10.12 4 53.67 50.33 38.00 46.17 60.83 55.67 5 1.67 1.83 1.171.67 2.67 2.83 6 24.00 43.67 30.33 30.33 38.33 40.00 7 9.00 8.67 9.119.89 7.67 17.56 8 1.11 4.38 1.44 1.44 4.56 1.67 9 16.89 16.25 13.2216.89 27.00 8.11 10 29.56 1.75 19.78 22.33 11.67 22.78 11 0.00 0.00 0.110.11 0.00 0.44 12 96.67 76.67 67.50 75.83 74.17 76.67 13 86.78 69.5662.44 70.89 69.44 63.89 14 2.87 1.38 2.13 2.26 2.60 1.87 15 0.89 0.900.87 0.89 2.32 0.37 16 2.33 3.50 3.00 2.17 2.83 2.00 17 89.00 219.3393.00 86.00 191.33 71.33 18 150.89 55.89 134.00 160.44 75.44 324.63 19123.56 43.89 87.67 102.67 93.56 88.00 20 1.56 3.00 1.78 1.78 5.67 5.6321 17.00 18.75 26.44 32.33 21.56 33.50 22 38.44 2.00 26.44 31.33 8.8982.00 23 0.00 0.00 0.00 0.00 0.00 1.50 24 16.56 16.78 16.11 18.11 16.7817.11 25 23.00 16.00 23.11 33.00 15.22 45.25 26 274.44 99.78 221.67263.11 169.00 412.50 27 67.78 63.78 64.89 74.89 54.00 167.22 28 26.0014.89 20.11 20.11 21.11 30.25 29 22.11 14.33 16.00 15.00 33.78 9.00 3048.11 29.22 36.11 35.11 54.89 38.88 31 15.09 10.50 17.23 16.51 12.0610.25 32 170.89 198.22 152.56 163.89 224.67 265.00 33 47.57 43.77 50.3756.30 44.00 40.33 34 2.67 1.95 2.43 2.53 2.13 2.68 35 2.60 1.89 2.522.53 2.17 2.59 36 5.24 4.15 3.91 3.92 4.15 3.74 37 57.00 28.56 54.6765.44 36.11 122.63 38 104.56 51.67 89.22 106.22 79.33 155.63 39 47.5623.11 34.56 40.78 43.22 33.00 40 89.00 93.00 86.00 71.33

TABLE 130 Measured parameters in Soybean varieties (lines 7-12) Ecotype/Treatment Line-7 Line-8 Line-9 Line-10 Line-11 Line-12 1 73.00 72.3368.67 73.67 68.00 70.67 2 66.50 65.67 62.33 67.67 61.67 64.33 3 8.468.09 8.26 7.73 8.16 7.89 4 48.00 52.00 44.17 52.67 56.00 47.50 5 2.672.50 1.83 3.50 3.33 1.50 6 41.00 38.33 31.00 39.00 27.33 32.67 7 11.6712.11 8.00 9.11 6.78 10.00 8 4.00 4.33 2.11 1.89 3.44 1.22 9 21.33 17.6720.33 16.11 28.11 16.56 10 11.11 28.22 24.11 36.44 39.67 32.33 11 0.000.56 0.00 3.89 0.00 0.00 12 101.67 98.33 75.83 116.67 76.67 71.67 1389.78 82.11 70.56 101.67 79.56 67.22 14 1.98 2.71 2.78 2.75 3.70 2.84 153.90 0.78 1.18 1.98 1.03 0.83 16 3.50 2.50 2.17 2.33 2.17 2.17 17 88.0075.00 80.67 75.67 76.33 77.33 18 46.88 176.22 143.00 105.44 184.33187.33 19 80.00 126.56 115.11 159.00 178.67 131.33 20 2.88 3.00 1.252.67 1.78 3.00 21 8.50 22.78 21.75 10.67 23.78 25.67 22 9.00 42.11 32.7525.67 45.00 44.33 23 0.00 0.33 0.00 1.11 0.00 0.00 24 18.78 18.89 16.7821.11 19.33 20.78 25 8.25 25.44 21.88 16.33 22.56 24.22 26 136.00 302.78260.50 264.44 363.00 318.67 27 45.44 83.22 64.33 52.00 76.89 67.00 284.13 20.11 17.00 9.22 28.11 22.56 29 9.03 16.00 15.89 14.56 30.44 18.0030 14.25 36.11 32.75 23.78 58.56 40.56 31 7.30 11.38 15.68 10.83 12.9815.16 32 160.67 196.33 155.33 178.11 204.44 164.22 33 34.23 44.27 53.6742.47 43.60 52.20 34 2.12 2.58 2.58 2.67 2.62 2.58 35 2.22 2.49 2.472.71 2.51 2.61 36 4.80 4.36 4.20 4.82 4.12 3.83 37 20.38 68.22 55.7540.11 70.56 73.00 38 61.00 119.00 103.25 98.44 141.78 123.11 39 36.4450.78 43.63 58.33 71.22 50.11 40 88.00 75.00 80.67 75.67 76.33 77.33Table 130.

TABLE 131 Measured parameters in Soybean varieties (lines 1-8) Ecotype/Treatment Line-1 Line-2 Line-3 Line-4 Line-5 Line-6 Line-7 Line-8 167.33 67.33 67.33 70.00 68.00 71.67 67.33 67.67 3 8.27 8.00 8.33 7.167.78 9.54 8.13 9.68 4 35.83 51.67 53.67 34.67 47.50 50.33 53.50 38.00 52.00 2.00 1.67 1.67 1.17 1.83 1.67 1.17 6 27.67 27.67 24.00 30.33 31.3343.67 27.00 30.33 7 5.11 8.44 9.00 7.00 8.67 8.67 7.11 9.11 8 0.56 2.441.11 2.56 0.89 4.38 1.89 1.44 9 16.44 17.22 16.89 25.33 10.44 16.2520.00 13.22 10 19.33 23.33 29.56 23.33 30.56 1.75 23.56 19.78 11 0.000.00 0.00 0.00 2.22 0.00 0.00 0.11 12 69.17 85.00 96.67 75.83 73.3376.67 75.00 67.50 13 66.78 79.44 86.78 64.11 68.00 69.56 74.11 62.44 142.34 2.67 2.87 2.87 2.51 1.38 2.65 2.13 15 1.28 1.13 0.89 1.35 0.86 0.901.43 0.87 16 3.00 2.17 2.33 2.33 2.50 3.50 2.67 3.00 17 126.00 116.0089.00 75.67 84.33 219.33 119.00 93.00 18 92.78 124.00 150.89 122.78174.89 55.89 112.67 134.00 19 91.44 106.89 123.56 123.22 122.33 43.89112.56 87.67 20 0.78 0.89 1.56 0.78 1.00 3.00 1.22 1.78 21 15.33 17.5617.00 23.33 18.11 18.75 21.22 26.44 22 20.44 29.33 38.44 25.11 43.222.00 23.00 26.44 23 0.000 0.000 0.000 0.000 2.000 0.000 0.000 0.000 2415.56 16.11 16.56 17.78 17.67 16.78 17.33 16.11 25 13.89 20.89 23.0022.44 26.11 16.00 21.56 23.11 26 184.22 230.89 274.44 246.00 297.2299.78 225.22 221.67 27 57.78 66.67 67.78 57.00 73.67 63.78 64.44 64.8928 23.00 25.00 26.00 18.33 23.22 14.89 27.89 20.11 29 22.56 22.22 22.1117.89 17.89 14.33 23.78 16.00 30 45.56 47.22 48.11 36.22 41.11 29.2251.67 36.11 31 21.35 14.70 15.09 13.44 16.60 10.50 16.03 17.23 32 158.89185.78 170.89 146.78 172.78 198.22 166.44 152.56 33 55.53 50.33 47.5746.83 55.87 43.77 51.67 50.37 34 2.53 2.58 2.67 2.51 2.74 1.95 2.46 2.4335 2.52 2.49 2.60 2.36 2.77 1.89 2.50 2.52 36 4.29 4.93 5.24 3.61 3.854.15 4.29 3.91 37 36.56 47.78 57.00 49.22 64.33 28.56 45.44 54.67 3872.89 90.78 104.56 100.44 108.44 51.67 90.89 89.22 39 36.33 43.00 47.5651.22 44.11 23.11 45.44 34.56 Table 131.

TABLE 132 Measured parameters in Soybean varieties (lines 9-16) Ecotype/Line- Line- Line- Line- Line- Line- Line- Treatment Line-9 10 11 12 1314 15 16 1 71.67 67.33 67.00 69.67 60.00 70.67 71.67 71.67 3 8.41 8.117.54 7.83 8.82 8.10 8.72 9.54 4 45.83 46.17 38.67 50.67 60.83 44.3352.33 54.50 5 1.83 1.67 1.17 2.67 2.67 1.50 3.00 1.83 6 35.33 30.3328.00 41.00 38.33 31.00 36.00 38.67 7 8.67 9.89 5.33 5.00 7.67 4.78 7.788.78 8 2.33 1.44 1.67 1.67 4.56 2.67 4.14 1.89 9 22.33 16.89 17.00 19.2227.00 32.89 18.71 15.11 10 25.44 22.33 31.89 10.00 11.67 27.89 31.4341.89 11 0.11 0.11 0.00 0.00 0.00 0.00 1.71 0.44 12 75.00 75.83 66.67115.83 74.17 72.50 83.33 76.67 13 69.67 70.89 62.33 94.44 69.44 66.7875.44 68.56 14 2.77 2.26 2.76 1.43 2.60 3.32 3.19 3.17 15 1.38 0.89 1.412.40 2.32 1.54 0.80 1.21 16 2.00 2.17 2.00 3.00 2.83 2.17 2.00 2.33 1784.67 86.00 75.67 169.33 191.33 86.67 85.67 87.67 18 171.11 160.44139.67 49.44 75.44 112.33 204.67 180.78 19 123.78 102.67 131.33 70.1193.56 152.11 140.11 159.56 20 2.78 1.78 0.89 0.33 5.67 1.56 5.13 0.67 2134.44 32.33 19.89 12.56 21.56 21.22 29.63 16.67 22 33.00 31.33 33.008.00 8.89 22.78 40.25 48.78 23 0.111 0.000 0.000 0.000 0.000 0.000 0.7500.111 24 18.00 18.11 18.33 21.56 16.78 19.11 17.33 18.78 25 26.33 33.0021.33 14.38 15.22 18.56 30.44 28.00 26 294.89 263.11 271.00 119.56169.00 264.44 344.78 340.33 27 80.33 74.89 58.33 55.25 54.00 52.44105.00 67.00 28 23.00 20.11 19.33 12.00 21.11 15.33 23.78 20.67 29 18.0015.00 19.63 15.41 33.78 21.56 16.22 26.56 30 41.00 35.11 39.88 27.4154.89 36.89 40.00 47.22 31 14.64 16.51 17.12 10.52 12.06 15.80 12.6412.58 32 175.67 163.89 136.56 191.67 224.67 155.33 216.22 192.11 3352.93 56.30 55.07 40.17 44.00 52.37 46.90 48.57 34 2.43 2.53 2.60 2.342.13 2.48 2.47 2.70 35 2.48 2.53 2.60 2.26 2.17 2.40 2.52 2.68 36 3.903.92 3.41 4.38 4.15 3.50 4.36 3.67 37 70.33 65.44 53.78 20.89 36.1145.56 83.11 66.22 38 120.56 106.22 104.33 51.78 79.33 109.00 138.89125.56 39 50.22 40.78 50.56 30.89 43.22 63.44 55.78 59.33 Table 132

TABLE 133 Measured parameters in Soybean varieties (lines 17-23)Ecotype/ Line- Line- Line- Line- Line- Line- Treatment Line-17 18 19 2021 22 23 1 74.00 73.00 72.33 73.33 67.33 68.67 69.33 3 10.12 8.46 8.098.11 7.09 8.26 7.57 4 55.67 48.00 52.00 45.17 57.00 44.17 43.33 5 2.832.67 2.50 1.67 2.50 1.83 2.00 6 40.00 41.00 38.33 37.00 24.67 31.0037.67 7 17.56 11.67 12.11 10.44 8.00 8.00 9.00 8 1.67 4.00 4.33 1.891.78 2.11 0.44 9 8.11 21.33 17.67 20.00 17.44 20.33 11.22 10 22.78 11.1128.22 27.89 25.11 24.11 25.22 11 0.44 0.00 0.56 0.56 0.44 0.00 0.11 1276.67 101.67 98.33 89.17 93.33 75.83 78.33 13 63.89 89.78 82.11 81.1185.67 70.56 70.78 14 1.87 1.98 2.71 2.58 2.45 2.78 2.15 15 0.37 3.900.78 1.36 0.92 1.18 0.82 16 2.00 3.50 2.50 2.00 2.50 2.17 2.17 17 71.3388.00 75.00 78.67 91.67 80.67 80.67 18 324.63 46.88 176.22 121.56 151.56143.00 144.00 19 88.00 80.00 126.56 127.78 113.78 115.11 99.00 20 5.632.88 3.00 2.33 1.67 1.25 0.89 21 33.50 8.50 22.78 21.89 22.89 21.7513.22 22 82.00 9.00 42.11 24.56 34.11 32.75 38.89 23 1.500 0.000 0.3330.444 0.444 0.000 0.000 24 17.11 18.78 18.89 19.44 19.89 16.78 17.00 2545.25 8.25 25.44 22.67 23.00 21.88 23.78 26 412.50 136.00 302.78 249.33265.33 260.50 243.00 27 167.22 45.44 83.22 63.67 69.67 64.33 76.22 2830.25 4.13 20.11 14.89 24.33 17.00 19.22 29 9.00 9.03 16.00 14.57 19.7815.89 14.67 30 38.88 14.25 36.11 29.46 44.11 32.75 33.89 31 10.25 7.3011.38 13.86 14.63 15.68 14.77 32 265.00 160.67 196.33 166.33 171.44155.33 175.78 33 40.33 34.23 44.27 46.23 49.70 53.67 52.53 34 2.68 2.122.58 2.48 2.61 2.58 2.70 35 2.59 2.22 2.49 2.53 2.53 2.47 2.67 36 3.744.80 4.36 4.18 4.89 4.20 4.16 37 122.63 20.38 68.22 49.22 59.11 55.7553.00 38 155.63 61.00 119.00 99.56 103.89 103.25 90.00 39 33.00 36.4450.78 50.33 44.78 46.56 37.00 Table 133.

TABLE 134 Measured parameters in Soybean varieties (lines 24-29)Ecotype/ Treatment Line-24 Line-25 Line-26 Line-27 Line-28 Line-29 173.67 68.00 68.67 68.00 67.00 70.67 3 7.73 8.16 8.18 6.88 7.82 7.89 452.67 56.00 56.17 43.50 46.00 47.50 5 3.50 3.33 1.83 1.50 2.33 1.50 639.00 27.33 27.67 27.33 36.33 32.67 7 9.11 6.78 7.11 4.33 9.11 10.00 81.89 3.44 3.22 1.67 3.33 1.22 9 16.11 28.11 24.67 14.67 14.33 16.56 1036.44 39.67 35.78 31.67 37.56 32.33 11 3.89 0.00 0.00 0.78 0.78 0.00 12116.67 76.67 85.00 78.33 79.17 71.67 13 101.67 79.56 77.44 73.67 73.6767.22 14 2.75 3.70 3.58 3.06 3.34 2.84 15 1.98 1.03 1.48 1.82 1.35 0.8316 2.33 2.17 2.17 2.33 2.17 2.17 17 75.67 76.33 88.00 93.33 79.00 77.3318 105.44 184.33 166.22 92.33 143.78 187.33 19 159.00 178.67 159.89129.11 147.78 131.33 20 2.67 1.78 1.00 0.56 2.11 3.00 21 10.67 23.7826.78 10.22 15.89 25.67 22 25.67 45.00 37.22 23.78 35.89 44.33 23 1.1110.000 0.000 0.000 0.556 0.000 24 21.11 19.33 17.78 15.89 16.67 20.78 2516.33 22.56 19.89 11.78 16.00 24.22 26 264.44 363.00 326.11 221.44291.56 318.67 27 52.00 76.89 74.78 35.33 52.11 67.00 28 9.22 28.11 24.2214.33 15.13 22.56 29 14.56 30.44 24.22 26.36 21.44 18.00 30 23.78 58.5648.44 40.69 35.75 40.56 31 10.83 12.98 16.38 16.64 15.82 15.16 32 178.11204.44 205.89 144.67 176.44 164.22 33 42.47 43.60 51.90 52.50 46.4352.20 34 2.67 2.62 2.37 2.67 2.62 2.58 35 2.71 2.51 2.53 2.64 2.65 2.6136 4.82 4.12 4.36 4.64 4.47 3.57 37 40.11 70.56 71.67 34.56 54.44 73.0038 98.44 141.78 135.33 83.33 110.44 123.11 39 58.33 71.22 63.67 48.7856.00 50.11 Table 134.

TABLE 135 Correlation between the expression level of selected genes ofsome embodiments of the invention in various tissues and the phenotypicperformance under normal conditions across 26 soybean varieties GeneExp. Corr. Gene Exp. Corr. Name R P value set Set ID Name R P value setSet ID LYD868 0.73 1.92E−05 3 31 LYD874 0.72 2.21E−05 10 19 LYD874 0.74.27E−05 10 10 LYD874 0.7 4.37E−05 10 39 LYD876 0.7 6.67E−05 6 31 LYD8770.76 3.69E−06 10 19 LYD877 0.72 2.37E−05 10 10 LYD877 0.74 1.06E−05 1039 LYD886 0.71 3.92E−05 10 31 LYD888 0.54 4.40E−03 3 19 LYD888 0.544.10E−03 3 14 LYD888 0.58 2.00E−03 3 39 Table 135. Provided are thecorrelations (R) between the expression levels yield improving genes andtheir homologs in various tissues [Expression (Exp) sets] and thephenotypic performance [yield, biomass, and plant architecture(Correlation vector (Corr.))] under normal conditions across soybeanvarieties. P = p value.

TABLE 136 Correlation between the expression level of selected genes ofsome embodiments of the invention in various tissues and the phenotypicperformance under normal conditions across 12 soybean varieties GeneExp. Corr. Gene Exp. Corr. Name R P value set Set ID Name R P value setSet ID LGP104 0.76 4.05E−03 11 10 LGP104 0.82 1.10E−03 11 19 LGP104 0.872.71E−04 11 14 LGP104 0.72 4.48E−02 9 24 LGP104 0.79 2.33E−03 11 39LYD879 0.74 6.39E−03 10 37 LGP105 0.73 1.70E−02 5 20 LGP105 0.751.32E−02 8 20 LGP105 0.75 3.22E−02 9 22 LGP105 0.75 3.08E−02 9 18 LGP1050.76 2.96E−02 9 21 LGP105 0.88 4.16E−03 9 32 LGP105 0.94 5.61E−04 9 23LGP105 0.95 3.31E−04 9 27 LGP105 0.79 1.96E−02 9 7 LGP105 0.88 3.99E−039 25 LGP105 0.82 1.33E−02 9 3 LGP105 0.71 4.83E−02 9 26 LGP105 0.857.65E−03 9 20 LGP105 0.86 3.28E−04 4 17 LGP105 0.72 4.60E−02 9 38 LYD8630.78 2.69E−03 10 35 LGP109 0.77 8.57E−03 5 3 LGP109 0.79 6.08E−03 5 20LGP109 0.82 3.82E−03 5 17 LGP109 0.89 2.89E−03 9 31 LGP109 0.88 3.86E−039 33 LGP78 0.71 2.26E−02 7 3 LGP78 0.83 3.10E−03 7 20 LGP78 0.741.41E−02 8 31 LGP78 0.74 3.70E−02 9 10 LGP78 0.80 1.63E−02 9 31 LGP780.75 3.38E−02 9 33 LGP78 0.72 8.04E−03 10 10 LGP78 0.71 9.99E−03 10 7LGP79 0.73 1.55E−02 8 31 LGP78 0.72 4.42E−02 9 34 MGP4 0.72 1.83E−02 835 LGP78 0.71 5.00E−02 5 40 LGP78 0.85 1.74E−03 1 40 LGP79 0.74 1.51E−028 33 LGP79 0.71 4.99E−02 9 10 LGP79 0.77 2.41E−02 9 30 LGP79 0.753.35E−02 9 28 LGP79 0.72 4.62E−02 9 26 LGP79 0.73 7.58E−03 10 33 LGP790.81 4.69E−03 7 35 LYD863 0.87 5.39E−03 9 34 LGP79 0.72 4.34E−02 9 34LYD866 0.73 6.85E−03 10 38 LGP81 0.72 4.56E−02 9 10 LGP81 0.88 3.91E−039 31 LGP81 0.71 4.97E−02 9 33 LGP81 0.77 2.60E−02 9 14 LGP81 0.724.50E−02 9 29 LYD860 0.71 5.02E−02 9 4 LGP81 0.71 1.02E−02 11 39 LYD8710.76 1.12E−02 5 34 LGP81 0.74 3.44E−02 5 40 LGP81 0.82 3.75E−03 1 40LYD860 0.71 9.06E−03 1 20 LYD860 0.75 4.64E−03 10 31 LYD860 0.741.54E−02 10 40 LYD861 0.75 3.25E−02 7 40 LYD861 0.82 3.39E−03 8 23LYD861 0.75 1.33E−02 8 27 LYD861 0.73 4.04E−02 9 24 LYD861 0.72 8.53E−0310 33 LYD863 0.72 1.88E−02 7 31 LYD863 0.80 1.79E−02 9 10 LYD863 0.893.09E−03 9 31 LYD863 0.86 5.61E−03 9 33 LYD863 0.71 4.94E−02 9 21 LYD8630.84 8.27E−03 9 30 LYD863 0.71 5.00E−02 9 14 LYD863 0.85 7.84E−03 9 28LYD863 0.73 4.05E−02 9 26 LYD863 0.71 1.02E−02 10 22 LYD864 0.731.58E−02 5 9 LYD863 0.78 2.29E−02 9 35 LYD873 0.79 2.16E−03 4 34 LYD8630.72 4.24E−02 9 38 LYD871 0.73 1.56E−02 5 35 LYD863 0.76 4.25E−03 10 34LYD886 0.77 9.58E−03 8 37 LYD864 0.79 6.93E−03 8 32 LYD864 0.70 2.40E−028 20 LYD864 0.90 2.27E−03 9 17 LYD864 0.73 7.31E−03 10 22 LYD864 0.782.98E−03 10 18 LYD864 0.72 8.55E−03 10 21 LYD864 0.85 4.87E−04 10 27LYD864 0.75 4.58E−03 10 7 LYD864 0.83 8.46E−04 10 25 LYD865 0.823.48E−03 5 32 LYD865 0.85 1.78E−03 5 4 LYD865 0.80 5.85E−03 8 17 LYD8650.78 2.36E−02 9 2 LYD865 0.73 4.14E−02 9 23 LYD865 0.73 3.89E−02 9 27LYD865 0.87 4.56E−03 9 7 LYD865 0.74 3.57E−02 9 1 LYD865 0.81 1.44E−02 93 LYD865 0.75 3.11E−02 9 20 LYD865 0.81 1.50E−03 1 16 LYD865 0.898.77E−05 1 17 LYD866 0.86 1.37E−03 8 32 LYD865 0.83 3.25E−03 1 40 LYD8670.83 1.10E−02 4 40 LYD866 0.71 2.06E−02 8 23 LYD866 0.87 1.11E−03 8 27LYD866 0.71 2.07E−02 8 7 LYD866 0.74 1.37E−02 8 25 LYD866 0.87 1.06E−038 3 LYD866 0.72 1.86E−02 8 20 LYD866 0.81 1.30E−03 4 32 LYD866 0.745.54E−03 1 27 LYD866 0.77 3.73E−03 1 7 LYD866 0.78 2.63E−03 10 22 LYD8660.82 1.15E−03 10 18 LYD866 0.76 4.39E−03 10 27 LYD866 0.75 4.84E−03 1025 LYD866 0.73 7.58E−03 10 26 LYD866 0.83 9.30E−04 10 37 LYD881 0.762.70E−02 9 38 LYD867 0.74 1.52E−02 8 22 LYD867 0.73 1.75E−02 8 18 LYD8670.77 8.66E−03 8 23 LYD867 0.71 2.19E−02 8 26 LYD867 0.79 1.89E−02 9 31LYD867 0.82 1.37E−02 9 33 LYD867 0.71 2.07E−02 8 37 LGP78 0.70 5.16E−029 35 LYD868 0.75 4.80E−03 11 2 LYD868 0.74 5.66E−03 11 13 LYD868 0.719.19E−03 11 12 LYD868 0.75 4.54E−03 11 1 LYD868 0.72 1.86E−02 5 4 LYD8680.71 2.04E−02 5 3 LYD868 0.84 2.13E−03 5 17 LYD868 0.75 1.24E−02 8 11LYD868 0.92 2.00E−04 8 23 LYD868 0.82 1.33E−02 9 9 LYD868 0.72 4.48E−029 14 LYD868 0.91 1.91E−03 9 29 LYD868 0.73 7.60E−03 4 24 LYD868 0.801.97E−03 1 11 LYD868 0.74 5.97E−03 10 31 LYD868 0.82 1.16E−03 10 33LYD869 0.72 1.97E−02 5 27 LYD869 0.76 1.07E−02 8 20 LYD869 0.76 1.02E−028 17 LYD870 0.77 9.07E−03 7 4 LYD869 0.76 3.03E−02 9 36 LYD889 0.782.69E−03 1 39 LYD869 0.84 1.74E−02 9 40 LYD871 0.73 1.72E−02 11 40LYD870 0.74 1.38E−02 7 20 LYD870 0.74 1.45E−02 8 21 LYD870 0.76 1.08E−028 32 LYD870 0.87 1.15E−03 8 23 LYD870 0.81 4.62E−03 8 27 LYD870 0.778.55E−03 8 7 LYD870 0.74 1.39E−02 8 25 LYD870 0.78 8.05E−03 8 20 LYD8700.73 4.01E−02 9 31 LYD870 0.80 1.64E−02 9 19 LYD870 0.86 5.80E−03 9 14LYD870 0.78 2.21E−02 9 29 LYD870 0.75 5.35E−03 1 27 LYD870 0.73 6.55E−031 25 LYD870 0.75 5.05E−03 1 26 LYD871 0.84 2.42E−03 7 4 LYD870 0.764.35E−03 1 38 LYD871 0.72 8.12E−03 10 35 LYD871 0.86 1.33E−03 5 10LYD871 0.79 7.08E−03 5 19 LYD871 0.78 8.01E−03 5 26 LYD871 0.73 4.16E−029 33 LYD871 0.71 4.82E−02 9 3 LYD871 0.84 6.05E−04 10 10 LYD871 0.792.40E−03 10 19 LYD872 0.71 1.02E−02 10 33 LYD871 0.71 2.04E−02 5 39LGP78 0.72 8.75E−03 10 35 LYD871 0.75 1.25E−02 5 38 LYD876 0.84 9.17E−039 36 LYD871 0.72 8.49E−03 10 34 LYD876 0.87 1.02E−03 5 39 LYD873 0.796.81E−03 7 31 LYD873 0.77 9.39E−03 7 33 LYD873 0.78 7.86E−03 8 23 LYD8730.75 3.04E−02 9 9 LYD873 0.82 1.28E−02 9 29 LYD873 0.70 1.11E−02 4 10LYD873 0.73 7.62E−03 4 22 LYD873 0.73 6.89E−03 4 26 LYD873 0.85 4.98E−0410 23 LYD874 0.73 1.58E−02 5 15 LYD873 0.75 4.84E−03 4 35 LYD863 0.702.28E−02 7 34 LYD874 0.79 1.90E−02 9 31 LYD874 0.80 1.81E−02 9 33 LYD8740.73 4.01E−02 9 19 LYD874 0.77 2.44E−02 9 14 LYD874 0.70 1.05E−02 1 14LYD874 0.74 6.44E−03 10 10 LYD874 0.79 2.25E−03 10 24 LYD874 0.755.21E−03 10 19 LYD874 0.72 8.28E−03 10 39 LYD877 0.78 3.02E−03 10 39LYD876 0.75 5.07E−03 11 10 LYD876 0.77 3.62E−03 11 19 LYD876 0.782.82E−03 11 14 LYD876 0.72 8.52E−03 11 23 LYD876 0.84 7.08E−04 11 27LYD876 0.71 1.02E−02 11 25 LYD876 0.79 2.08E−03 11 20 LYD876 0.852.06E−03 5 15 LYD876 0.90 4.36E−04 5 10 LYD876 0.91 2.44E−04 5 19 LYD8760.76 1.04E−02 5 14 LYD876 0.79 6.36E−03 5 23 LYD876 0.77 9.56E−03 8 32LYD876 0.96 9.16E−06 8 3 LYD876 0.73 4.11E−02 9 15 LYD876 0.72 4.20E−029 16 LYD876 0.75 3.07E−02 9 13 LYD876 0.81 1.58E−02 9 12 LYD876 0.733.90E−02 9 7 LYD876 0.84 8.87E−03 9 17 LYD876 0.71 1.54E−02 2 19 LYD8760.82 1.24E−03 4 15 LYD876 0.80 1.85E−03 4 32 LYD876 0.71 9.23E−03 4 4LYD876 0.88 1.81E−04 4 20 LYD876 0.71 9.67E−03 1 3 LYD876 0.73 1.58E−025 34 LYD891 0.72 1.91E−02 5 36 LYD876 0.81 4.55E−03 5 35 LYD870 0.801.65E−02 9 39 LYD876 0.72 1.22E−02 2 39 MGP4 0.75 3.16E−02 9 39 LYD8760.85 1.66E−02 9 40 LYD877 0.81 1.50E−02 8 40 LYD877 0.85 7.81E−03 9 15LYD877 0.80 2.00E−03 10 10 LYD877 0.79 2.23E−03 10 24 LYD877 0.811.39E−03 10 19 LYD878 0.77 2.53E−02 7 40 LYD878 0.77 4.17E−02 9 40LYD879 0.73 1.61E−02 7 21 LYD879 0.87 4.72E−03 9 17 LYD879 0.74 6.06E−0310 22 LYD879 0.74 5.61E−03 10 18 LYD879 0.73 1.66E−02 8 39 LYD889 0.861.41E−03 8 37 LYD880 0.75 1.29E−02 5 11 LYD880 0.88 8.00E−04 5 23 LYD8800.86 1.56E−03 8 32 LYD880 0.76 1.00E−02 8 23 LYD880 0.77 9.08E−03 8 27LYD880 0.73 1.70E−02 8 3 LYD880 0.83 2.92E−03 8 20 LYD880 0.79 1.94E−029 6 LYD880 0.87 5.43E−03 9 3 LYD880 0.76 3.82E−03 1 32 LYD880 0.854.65E−04 1 27 LYD880 0.80 1.98E−03 1 3 LYD881 0.73 1.57E−02 7 20 LYD8810.78 2.37E−02 9 22 LYD881 0.82 1.18E−02 9 18 LYD881 0.89 3.24E−03 9 21LYD881 0.76 2.81E−02 9 32 LYD881 0.71 4.87E−02 9 23 LYD881 0.82 1.31E−029 27 LYD881 0.81 1.38E−02 9 25 LYD881 0.74 3.54E−02 9 26 LYD881 0.728.57E−03 10 33 LYD881 0.84 8.99E−03 9 37 LYD890 0.76 4.26E−03 10 38LYD882 0.74 1.49E−02 5 3 LYD882 0.72 1.93E−02 8 26 LYD882 0.75 3.32E−029 31 LYD882 0.77 2.59E−02 9 33 LYD882 0.79 2.04E−03 1 27 LYD882 0.801.90E−03 1 3 LYD882 0.76 4.33E−03 1 28 LYD882 0.70 1.06E−02 10 29 LYD8820.71 2.18E−02 8 38 LGP105 0.78 2.31E−02 9 37 LYD882 0.71 2.09E−02 11 40LYD884 0.71 4.91E−02 8 40 LYD883 0.71 2.18E−02 7 28 LYD883 0.71 4.99E−029 10 LYD883 0.71 4.91E−02 9 31 LYD883 0.77 2.62E−02 9 33 LYD883 0.743.71E−02 9 19 LYD883 0.76 2.79E−02 9 14 LYD883 0.73 7.21E−03 10 22LYD883 0.73 6.58E−03 10 2 LYD883 0.71 1.03E−02 10 1 LYD884 0.72 1.89E−027 20 LYD884 0.81 4.53E−03 8 15 LYD886 0.72 7.67E−03 11 27 LYD886 0.741.43E−02 5 20 LYD886 0.74 1.51E−02 8 18 LYD886 0.78 8.44E−03 8 21 LYD8860.88 9.14E−04 8 32 LYD886 0.89 6.27E−04 8 27 LYD886 0.75 1.29E−02 8 7LYD886 0.83 3.13E−03 8 25 LYD886 0.82 4.07E−03 8 3 LYD886 0.83 2.99E−038 20 LYD886 0.71 4.63E−02 9 31 LYD886 0.75 8.42E−03 2 32 LYD886 0.784.86E−03 2 20 LYD886 0.78 4.84E−03 2 17 LYD886 0.85 4.67E−04 1 32 LYD8860.80 1.87E−03 1 27 LYD886 0.73 7.36E−03 10 31 LYD886 0.73 6.67E−03 10 33LYD886 0.72 8.68E−03 10 21 LYD887 0.87 1.15E−03 7 15 LYD887 0.779.35E−03 5 9 LYD887 0.72 1.78E−02 5 19 LYD887 0.80 5.65E−03 5 14 LYD8870.90 3.83E−04 8 17 LYD889 0.78 7.86E−03 5 6 LYD887 0.81 4.54E−03 5 39LYD891 0.70 1.05E−02 1 37 LYD876 0.73 6.90E−03 11 39 LYD890 0.904.12E−04 7 15 LYD890 0.87 4.56E−03 9 15 LYD890 0.80 1.83E−03 10 22LYD890 0.81 1.48E−03 10 18 LYD890 0.77 3.18E−03 10 25 LYD890 0.773.27E−03 10 26 LYD890 0.80 1.79E−03 10 37 LYD873 0.72 4.22E−02 9 39LYD891 0.91 2.57E−04 7 13 LYD891 0.92 1.76E−04 7 12 LYD891 0.75 1.28E−025 3 LYD891 0.75 1.32E−02 8 32 LYD891 0.85 1.70E−03 8 3 LYD891 0.741.43E−02 8 20 LYD891 0.78 2.12E−02 9 15 LYD891 0.78 2.37E−02 9 3 LYD8910.80 3.10E−03 2 17 LYD891 0.73 7.12E−03 4 19 LYD891 0.76 4.02E−03 1 27LYD891 0.74 6.21E−03 10 21 LYD891 0.77 3.18E−03 10 13 LYD933 0.702.35E−02 7 31 LYD891 0.70 2.40E−02 7 36 LYD864 0.80 1.92E−03 10 37LYD891 0.76 4.00E−03 4 39 LGP79 0.71 4.95E−02 9 38 LYD891 0.93 7.68E−045 40 LYD891 0.71 4.75E−02 8 40 LYD867 0.79 7.10E−03 8 35 MGP4 0.861.24E−03 8 11 MGP4 0.73 1.59E−02 8 23 MGP4 0.76 2.77E−02 9 10 MGP4 0.791.93E−02 9 31 MGP4 0.80 1.68E−02 9 30 MGP4 0.78 2.27E−02 9 19 MGP4 0.849.56E−03 9 14 MGP4 0.86 6.22E−03 9 29 MGP4 0.80 1.63E−03 4 15 LGP79 0.823.81E−03 7 34 Table 136. Provided are the correlations (R) between theexpression levels yield improving genes and their homologs in varioustissues [Expression (Exp) sets] and the phenotypic performance [yield,biomass, and plant architecture (Correlation vector (Corr.))] undernormal conditions across soybean varieties. P = p value.

Example 17 Production of Tomato Transcriptome and High ThroughputCorrelation Analysis Using 44K Tomato Oligonucleotide Micro-Array

In order to produce a high throughput correlation analysis between NUErelated phenotypes and gene expression, the present inventors utilized aTomato oligonucleotide micro-array, produced by Agilent Technologies[chem. (dot) agilent (dot) com/Scripts/PDS (dot) asp?1Page=50879]. Thearray oligonucleotide represents about 44,000 Tomato genes andtranscripts. In order to define correlations between the levels of RNAexpression with NUE, ABST, yield components or vigor related parametersvarious plant characteristics of 18 different Tomato varieties wereanalyzed. Among them, 10 varieties encompassing the observed variancewere selected for RNA expression analysis. The correlation between theRNA levels and the characterized parameters was analyzed using Pearsoncorrelation test [davidmlane (dot) com/hyperstat/A34739 (dot) html].

Correlation of Tomato Varieties Across Ecotypes Grown Under LowNitrogen, Drought and Regular Growth Conditions

Experimental Procedures:

10 Tomato varieties were grown in 3 repetitive blocks, each containing 6plants per plot were grown at net house. Briefly, the growing protocolwas as follows:

1. Regular growth conditions: Tomato varieties were grown under normalconditions: 4-6 Liters/m² of water per day and fertilized with NPK(nitrogen, phosphorous and potassium at a ratio 6:6:6, respectively) asrecommended in protocols for commercial tomato production.

2. Low Nitrogen fertilization conditions: Tomato varieties were grownunder normal conditions (4-6 Liters/m² per day and fertilized with NPKas recommended in protocols for commercial tomato production) untilflower stage. At this time, Nitrogen fertilization was stopped.

3. Drought stress: Tomato variety was grown under normal conditions (4-6Liters/m² per day) until flower stage. At this time, irrigation wasreduced to 50% compared to normal conditions.

Plants were phenotyped on a daily basis following the standarddescriptor of tomato (Table 138). Harvest was conducted while 50% of thefruits were red (mature). Plants were separated to the vegetative partand fruits, of them, 2 nodes were analyzed for additional inflorescentparameters such as size, number of flowers, and inflorescent weight.Fresh weight of all vegetative material was measured. Fruits wereseparated to colors (red vs. green) and in accordance with the fruitsize (small, medium and large). Next, analyzed data was saved to textfiles and processed using the JMP statistical analysis software (SASinstitute). Data parameters collected are summarized in Tables 139-141,herein below.

Analyzed Tomato tissues—Two tissues at different developmental stages[flower and leaf], representing different plant characteristics, weresampled and RNA was extracted as described above. For convenience, eachmicro-array expression information tissue type has received a Set ID assummarized in Table 137 below.

TABLE 137 Tomato transcriptome expression sets Expression Set Set IDLeaf at reproductive stage under normal conditions 1 Flower under normalconditions 2 Leaf at reproductive stage under low N conditions 3 Flowerunder low N conditions 4 Leaf at reproductive stage under droughtconditions 5 Flower under drought conditions 6 Table 137: Provided arethe identification (ID) digits of each of the tomato expression sets.

The collected data parameters were as follows: Fruit Weight (gr)—At theend of the experiment [when 50% of the fruits were ripe (red)] allfruits from plots within blocks A-C were collected. The total fruitswere counted and weighted. The average fruits weight was calculated bydividing the total fruit weight by the number of fruits.

Yield/SLA—Fruit yield divided by the specific leaf area, gives ameasurement of the balance between reproductive and vegetativeprocesses.

Yield/total leaf area—Fruit yield divided by the total leaf area, givesa measurement of the balance between reproductive and vegetativeprocesses.

Plant vegetative Weight (FW) (gr)—At the end of the experiment [when 50%of the fruit were ripe (red)] all plants from plots within blocks A-Cwere collected. Fresh weight was measured (grams).

Inflorescence Weight (gr)—At the end of the experiment [when 50% of thefruits were ripe (red)] two Inflorescence from plots within blocks A-Cwere collected. The Inflorescence weight (gr.) and number of flowers perinflorescence were counted.

SPAD—Chlorophyll content was determined using a Minolta SPAD 502chlorophyll meter and measurement was performed at time of flowering.SPAD meter readings were done on young fully developed leaf. Threemeasurements per leaf were taken per plot.

Water use efficiency (WUE)—can be determined as the biomass produced perunit transpiration. To analyze WUE, leaf relative water content wasmeasured in control and transgenic plants. Fresh weight (FW) wasimmediately recorded; then leaves were soaked for 8 hours in distilledwater at room temperature in the dark, and the turgid weight (TW) wasrecorded. Total dry weight (DW) was recorded after drying the leaves at60° C. to a constant weight. Relative water content (RWC) was calculatedaccording to the following Formula I as described above.

Plants that maintain high relative water content (RWC) compared tocontrol lines were considered more tolerant to drought than thoseexhibiting reduced relative water content.

TABLE 138 Tomato correlated parameters (vectors) Correlated parameterwith Correlation ID 100 weight green fruit [gr.] (Drought) 1 100 weightgreen fruit [gr.] (Low N) 2 100 weight green fruit [gr.] (Normal) 3 100weight red fruit [gr.] (Drought) 4 100 weight red fruit [gr.] (Low N) 5100 weight red fruit [gr.] (Normal) 6 Cluster Weight (Low N/Normal) 7 FWNUE [gr.] (Normal) 8 FW (Drought/Normal) 9 FW/Plant [gr./number] (Low N)10 FW/Plant [gr./number] (Normal) 11 FW/Plant [gr./number] (Drought) 12Fruit (Drought/Low N) 13 Fruit NUE [number] (Normal) 14 Fruit Yield(Drought/Normal) 15 Fruit Yield/Plant [gr./number] (Low N) 16 FruitYield/Plant [gr./number] (Drought) 17 Fruit yield/Plant [gr.] (Normal)18 HI [yield/yield + biomass] (Low N) 19 HI [yield/yield + biomass](Normal) 20 Leaflet Length [cm] (Low N) 21 Leaflet Length [cm] (Normal)22 Leaflet Length [cm]) (Drought) 23 Leaflet Width [cm] (Low N) 24Leaflet Width [cm] (Normal) 25 Leaflet Width [cm] (Drought) 26 NUE[yield/SPAD] (Low N) 27 NUE [yield/SPAD] [gr./number] (Normal) 28 NUE2[total biomass/SPAD] (Low N) 29 NUE2 [total biomass/SPAD] [gr./number](Normal) 30 NUpE [biomass/SPAD] (Low N) 31 NUpE [biomass/SPAD][gr./number] (Normal) 32 No flowers (Low N) 33 Number of flowers(Normal) 34 Number of Flower Drought/Low N 35 Number of FlowerDrought/Normal 36 Number of flowers (Drought) 37 Num. Flowers (LowN/Normal) 38 RWC (Normal) 39 RWC Drought 40 RWC Drought/Normal 41 RWC(Low N) 42 RWC (Low N/Normal) 43 SPAD 100% RWC (Low N/Normal) 44 SLA[leaf area/plant biomass] [cm²/gr] (Low N) 45 SLA [leaf area/plantbiomass] [cm²/gr] (Normal) 46 SPAD (Normal) 47 SPAD 100% RWC (Low N) 48SPAD 100% RWC (Normal) 49 SPAD (Low N) 50 SPAD (Low N/Normal) 51 TotalLeaf Area [cm²] (Low N) 52 Total Leaf Area [cm²] (Normal) 53 Total LeafArea [cm²]) (Drought) 54 Weight Flower clusters [gr.] (Normal) 55 Weightclusters (flowers) (Low N) 56 Weight flower clusters [gr.] (Drought) 57Yield/SLA [gr./(cm²/gr.)] (Low N) 58 Yield/SLA [gr./(cm²/gr.)] (Normal)59 Yield/total leaf area [gr/cm²] (Low N) 60 Yield/total leaf area[gr./cm²] (Normal) 61 Average red fruit weight [gr.] (Low N) 62 Averagered fruit weight [gr.] (Normal) 63 Average red fruit weight [gr.](Drought) 64 Flower cluster weight Drought/Low N 65 Flower clusterweight Drought/Normal 66 Red fruit weight (Drought/Normal) 67 Table 138.Provided are the tomato correlated parameters. “gr.” = grams; “FW” =fresh weight; “NUE” = nitrogen use efficiency; “RWC” = relative watercontent; “NUpE” = nitrogen uptake efficiency; “SPAD” = chlorophylllevels; “HI” = harvest index (vegetative weight divided on yield); “SLA”= specific leaf area (leaf area divided by leaf dry weight), Treatmentin the parenthesis.

Experimental Results

Table 138 provides the tomato correlated parameters (Vectors). Theaverage for each of the measured parameter was calculated using the JMPsoftware and values are summarized in Tables 139-141 below. Subsequentcorrelation analysis was conducted

(Table 142). Results were integrated to the database.

TABLE 139 Measured parameters in Tomato accessions (lines 1-6) Ecotype/Treatment Line-1 Line-2 Line-3 Line-4 Line-5 Line-6 1 2 0.57 0.37 3.400.68 0.45 0.47 3 0.56 3.05 0.24 2.58 6.32 5.75 4 5 0.65 0.53 7.17 0.440.55 6 0.82 2.46 0.50 2.76 5.32 5.24 7 0.44 0.01 1.08 0.02 0.37 0.81 80.74 3.01 0.83 1.54 3.70 1.22 9 0.61 2.63 1.18 1.36 4.02 1.01 10 2.252.54 1.85 3.06 3.13 2.54 11 3.02 0.84 2.24 1.98 0.85 2.09 12 1.85 2.222.63 2.71 3.41 2.11 13 1.32 0.76 1.51 0.71 5.06 0.89 14 0.97 3.80 2.780.78 0.02 1.16 15 1.27 2.88 4.20 0.55 0.09 1.03 16 0.48 0.46 1.35 0.350.01 0.51 17 0.63 0.35 2.04 0.25 0.05 0.45 18 0.49 0.12 0.49 0.45 0.530.44 19 0.18 0.15 0.42 0.10 0.00 0.17 20 0.14 0.12 0.18 0.19 0.38 0.1721 3.69 5.43 6.95 3.73 4.39 6.72 22 6.34 7.99 5.59 7.70 7.85 6.22 23 241.79 2.55 3.52 1.73 1.87 3.54 25 3.69 4.77 3.43 4.56 4.44 3.15 26 270.01 0.02 0.04 0.01 0.00 0.02 28 0.009 0.003 0.010 0.010 0.012 0.008 290.08 0.13 0.09 0.11 0.11 0.09 30 0.063 0.021 0.057 0.056 0.032 0.047 310.07 0.11 0.05 0.09 0.11 0.08 32 0.054 0.018 0.046 0.046 0.020 0.039 339.00 13.00 10.67 16.67 6.00 16.00 34 6.33 7.67 9.67 8.33 5.00 8.33 351.74 1.56 1.09 1.52 4.96 1.08 36 2.47 2.65 1.21 3.04 5.95 2.08 37 15.6720.33 11.67 25.33 29.73 17.33 38 1.42 1.70 1.10 2.00 1.20 1.92 39 64.2967.07 54.79 77.61 58.18 66.51 40 65.33 72.22 66.13 68.33 78.13 18.46 411.02 1.08 1.21 0.88 1.34 0.28 42 69.49 63.24 77.36 77.91 80.49 67.40 431.08 0.94 1.41 1.00 1.38 1.01 44 0.92 0.75 1.31 0.97 1.11 0.95 45 131.29148.82 257.51 64.34 144.60 246.05 46 140.99 689.67 130.22 299.12 1117.74111.77 47 55.80 46.40 48.20 43.40 42.90 53.30 48 33.01 23.42 34.53 32.5127.66 33.68 49 35.89 31.09 26.38 33.68 24.98 35.47 50 47.50 37.00 44.6041.70 34.40 50.00 51 0.85 0.80 0.93 0.96 0.80 0.94 52 294.83 378.00476.39 197.08 453.24 625.51 53 426.10 582.38 291.40 593.58 947.59 233.3554 55 0.69 56.35 0.44 11.31 0.79 0.58 56 0.31 0.35 0.47 0.25 0.29 0.4757 0.33 0.29 0.55 0.31 0.45 0.56 58 0.004 0.003 0.005 0.006 0.000 0.00259 0.004 0.000 0.004 0.002 0.000 0.004 60 0.002 0.001 0.003 0.002 0.0000.001 61 0.001 0.000 0.002 0.001 0.001 0.002 62 0.006 0.005 0.096 0.0040.006 0.007 63 0.01 0.29 0.01 0.05 0.23 0.29 64 0.209 0.005 0.102 0.0020.035 0.006 65 1.06 0.82 1.16 1.25 1.52 1.19 66 0.47 0.01 1.25 0.03 0.560.96 67 25.38 0.02 20.26 0.04 0.15 0.02 Table 139.

TABLE 140 Measured parameters in Tomato accessions (lines 7-12) Ecotype/Treatment Line-7 Line-8 Line-9 Line-10 Line-11 Line-12 1 0.80 0.28 0.382 0.54 0.39 0.97 0.91 0.36 0.35 3 0.38 0.30 1.95 2.53 1.42 2.03 4 0.890.35 0.63 5 0.75 0.58 1.27 1.34 0.52 0.57 6 0.61 0.66 2.70 0.70 2.644.67 7 0.55 0.36 0.95 0.80 0.34 0.61 8 0.58 0.55 1.06 0.49 1.31 1.36 90.61 0.64 0.95 0.51 1.17 1.94 10 1.84 1.52 1.91 1.86 2.47 2.62 11 3.212.75 1.81 3.77 1.89 1.93 12 1.95 1.76 1.72 1.92 2.21 3.73 13 0.67 2.170.38 1.27 0.84 1.51 14 2.07 1.51 2.41 2.06 0.38 1.64 15 1.39 3.28 0.912.62 0.32 2.48 16 0.44 0.47 1.59 0.39 0.32 0.45 17 0.29 1.02 0.60 0.490.27 0.68 18 0.21 0.31 0.66 0.19 0.85 0.27 19 0.19 0.24 0.45 0.17 0.120.15 20 0.06 0.10 0.27 0.05 0.31 0.12 21 6.66 4.39 3.90 5.29 6.32 5.1122 6.16 5.65 4.39 4.44 6.77 7.42 23 5.15 3.38 7.14 24 3.28 2.52 2.612.61 3.58 2.56 25 3.37 3.13 2.40 2.02 3.80 3.74 26 2.55 2.04 4.17 270.01 0.01 0.06 0.01 0.01 0.02 28 0.004 0.006 0.017 0.004 0.015 0.006 290.08 0.06 0.14 0.06 0.06 0.12 30 0.058 0.060 0.062 0.083 0.047 0.046 310.06 0.04 0.08 0.05 0.05 0.10 32 0.055 0.054 0.045 0.079 0.033 0.040 3315.00 6.00 17.00 13.00 8.67 9.33 34 10.00 7.00 9.00 8.00 5.33 8.00 350.98 4.94 0.88 0.79 2.12 1.29 36 1.47 4.24 1.67 1.29 3.44 1.50 37 14.6729.67 15.00 10.33 18.33 12.00 38 1.50 0.86 1.89 1.63 1.63 1.17 39 64.7175.25 66.23 63.21 56.77 35.96 40 73.21 62.50 67.21 75.76 62.82 70.69 411.13 0.83 1.01 1.20 1.11 1.97 42 67.16 66.07 69.57 69.30 100.00 57.66 431.04 0.88 1.05 1.10 1.76 1.60 44 0.79 0.92 0.94 1.36 1.44 1.50 45 405.55299.32 86.19 182.32 160.18 90.10 46 106.29 123.14 104.99 111.88 307.95419.37 47 58.50 51.10 40.00 47.60 57.90 48.30 48 30.04 35.50 24.81 40.7747.47 26.06 49 37.87 38.43 26.49 30.07 32.89 17.35 50 44.70 53.70 35.7058.80 47.50 45.20 51 0.76 1.05 0.89 1.24 0.82 0.94 52 748.01 453.96164.85 338.30 396.00 236.15 53 340.73 339.11 190.14 421.79 581.33 807.5154 337.63 130.78 557.93 55 0.73 0.83 0.86 0.50 1.02 0.70 56 0.40 0.300.82 0.40 0.35 0.43 57 0.304 0.315 0.308 0.311 8.360 0.288 58 0.0010.002 0.018 0.002 0.002 0.005 59 0.002 0.003 0.006 0.002 0.003 0.001 600.001 0.001 0.010 0.001 0.001 0.002 61 0.001 0.001 0.003 0.000 0.0010.000 62 0.006 0.013 0.021 0.005 0.006 0.047 63 0.006 0.007 0.058 0.0070.026 0.261 64 0.005 0.005 0.005 0.012 0.005 0.006 65 0.76 1.04 0.380.78 24.12 0.67 66 0.42 0.38 0.36 0.62 8.20 0.41 67 0.86 0.74 0.09 1.720.17 0.02 Table 140.

TABLE 141 Measured parameters in Tomato accessions (lines 13-18)Ecotype/ Treatment Line-13 Line-14 Line-15 Line-16 Line-17 Line-18 10.63 2.86 1.16 4.40 2 0.57 4.38 2.02 8.13 0.87 3.66 3 1.39 2.27 0.450.42 4 2.27 7.40 2.94 11.60 5 0.94 6.17 3.67 11.33 1.06 6.87 6 2.17 0.490.34 0.75 7 0.94 0.68 0.40 1.44 0.46 1.07 8 0.51 0.71 0.31 0.47 2.650.38 9 0.35 1.06 0.21 0.48 1.72 0.34 10 1.08 1.17 0.92 1.09 4.04 1.21 112.14 1.65 3.01 2.29 1.53 3.17 12 0.75 1.76 0.63 1.11 2.62 1.09 13 0.981.34 0.38 0.84 1.15 0.73 14 0.41 1.21 4.59 1.70 0.49 1.93 15 0.41 1.621.76 1.42 0.57 1.41 16 0.14 0.40 1.44 0.50 0.41 0.66 17 0.14 0.53 0.550.41 0.47 0.48 18 0.35 0.33 0.31 0.29 0.83 0.34 19 0.12 0.25 0.61 0.310.09 0.35 20 0.14 0.17 0.09 0.11 0.35 0.10 21 4.72 6.83 7.10 8.21 6.405.92 22 6.71 5.87 4.16 10.29 23 5.48 8.62 6.35 6.77 24 2.48 3.43 3.303.69 3.47 1.97 25 2.98 3.22 2.09 5.91 26 3.09 4.69 3.87 2.91 27 0.000.01 0.04 0.01 0.01 0.02 28 0.008 0.006 0.008 0.005 0.017 0.009 29 0.030.05 0.06 0.04 0.16 0.05 30 0.057 0.036 0.080 0.044 0.047 0.095 31 0.030.04 0.02 0.03 0.14 0.03 32 0.049 0.030 0.072 0.039 0.031 0.085 33 12.676.67 9.33 8.00 19.00 5.33 34 7.67 9.00 10.67 9.00 5.67 19.33 35 1.611.90 1.36 1.42 0.88 1.22 36 2.65 1.41 1.19 1.26 2.94 0.34 37 20.33 12.6712.67 11.33 16.67 6.50 38 1.65 0.74 0.88 0.89 3.35 0.28 39 77.62 100.0063.16 75.13 72.83 76.47 40 55.75 75.22 63.68 62.31 72.12 74.51 41 0.720.75 1.01 0.83 0.99 0.97 42 90.79 68.00 59.65 72.17 74.07 99.08 43 1.170.68 0.94 0.96 1.02 1.30 44 1.05 0.56 1.48 0.84 0.79 1.37 45 160.99379.03 531.08 650.68 140.04 317.12 46 365.81 212.93 84.94 469.87 4743.60 54.50 41.60 59.10 49.70 37.20 48 35.38 30.60 38.97 37.46 28.4739.04 49 33.82 54.47 26.25 44.43 36.17 28.45 50 39.00 45.00 65.30 51.9038.40 39.40 51 0.89 0.83 1.57 0.88 0.77 1.06 52 174.58 441.78 489.18707.80 565.93 384.77 53 784.06 351.80 255.78 1078.10 54 176.67 791.86517.05 832.27 55 0.38 0.66 0.70 0.33 1.17 0.34 56 0.35 0.45 0.28 0.470.53 0.37 57 0.34 0.44 0.27 0.43 0.37 0.41 58 0.001 0.001 0.003 0.0010.003 0.002 59 0.001 0.002 0.004 0.001 60 0.001 0.001 0.003 0.001 0.0010.002 61 0.000 0.001 0.001 0.000 62 0.357 0.037 0.626 0.024 0.191 630.029 0.005 0.003 0.009 0.048 0.008 64 0.30 0.14 0.04 0.09 0.01 0.19 650.97 0.99 0.95 0.91 0.69 1.11 66 0.91 0.67 0.38 1.31 0.32 1.19 67 10.5027.89 11.79 9.98 0.19 24.37 Table 141: Provided are the values of eachof the parameters (as described above) measured in tomato accessions(Seed ID) under all growth conditions. Growth conditions are specifiedin the experimental procedure section.

TABLE 142 Correlation between the expression level of selected genes ofsome embodiments of the invention in various tissues and the phenotypicperformance under normal and stress conditions across tomato ecotypesGene Exp. Corr. Gene Exp. Corr. Name R P value set Set ID Name R P valueset Set ID LGP107 0.73 1.67E−02 3 48 LGP32 0.75 2.09E−02 2 32 LGP32 0.861.54E−03 5 40 LGP34 0.72 2.82E−02 1 32 LGP34 0.79 6.53E−03 4 38 LGP420.83 1.09E−02 2 22 LGP34 0.74 2.35E−02 1 30 LGP34 0.82 3.60E−03 4 29LGP34 0.79 6.61E−03 4 31 LGP34 0.76 1.06E−02 4 33 LGP34 0.75 1.30E−02 456 LGP34 0.72 1.82E−02 4 8 LGP42 0.82 1.26E−02 2 46 LGP42 0.87 4.97E−032 53 LGP42 0.85 7.98E−03 2 25 LGP42 0.83 2.84E−03 2 55 LYD892 0.886.82E−04 1 63 LYD892 0.73 1.76E−02 5 9 LYD892 0.71 2.23E−02 3 50 LYD8920.88 7.09E−04 2 55 LYD892 0.78 7.71E−03 2 63 LYD892 0.84 2.64E−03 1 55LYD893 0.82 6.41E−03 1 20 LYD893 0.95 2.49E−05 5 35 LYD894 0.71 4.93E−022 22 LYD894 0.85 7.34E−03 2 46 LYD894 0.85 1.90E−03 5 9 LYD895 0.811.53E−02 2 61 LYD894 0.78 2.37E−02 2 53 LYD894 0.71 2.22E−02 6 12 LYD8940.84 2.34E−03 6 9 LYD894 0.79 6.15E−03 5 12 LYD895 0.88 7.77E−04 5 37LYD895 0.79 6.33E−03 5 36 LYD895 0.89 6.48E−04 4 50 LYD895 0.90 3.33E−045 35 LYD895 0.73 1.66E−02 4 19 LYD895 0.73 1.63E−02 4 14 LYD895 0.842.57E−03 4 51 LYD895 0.73 2.49E−02 4 62 LYD897 0.70 2.38E−02 4 52 LYD8980.79 7.08E−03 1 55 LYD898 0.80 5.34E−03 6 12 LYD899 0.77 1.49E−02 2 30LYD899 0.90 1.06E−03 2 32 LYD899 0.73 1.56E−02 6 40 LYD901 0.75 1.16E−024 27 LYD901 0.70 2.34E−02 4 60 LYD901 0.72 1.79E−02 4 16 LYD902 0.751.21E−02 3 48 LYD902 0.72 1.88E−02 2 49 LYD902 0.74 1.34E−02 5 9 LYD9030.72 1.85E−02 6 35 LYD903 0.91 2.11E−04 6 37 LYD903 0.90 3.97E−04 6 36LYD903 0.73 1.59E−02 5 65 LYD903 0.72 1.77E−02 5 57 LYD904 0.73 1.71E−025 65 LYD904 0.81 4.71E−03 5 66 LYD904 0.74 1.42E−02 5 57 LYD905 0.842.62E−03 3 58 LYD906 0.88 1.93E−03 1 32 LYD905 0.81 4.29E−03 2 55 LYD9050.88 7.46E−04 2 39 LYD906 0.87 2.55E−03 1 30 LYD906 0.72 2.85E−02 2 30LYD906 0.71 2.04E−02 1 11 LYD906 0.75 1.25E−02 1 34 LYD907 0.81 1.58E−022 59 LYD907 0.75 3.19E−02 2 61 LYD907 0.77 9.12E−03 6 9 LYD907 0.731.61E−02 5 9 LYD907 0.70 2.33E−02 2 63 LYD907 0.71 2.03E−02 1 63 LYD9080.71 2.14E−02 1 34 LYD909 0.72 1.98E−02 6 35 LYD910 0.84 2.18E−03 4 33LYD911 0.76 1.03E−02 3 42 LYD910 0.72 1.98E−02 2 55 LYD910 0.75 1.31E−021 55 LYD911 0.74 3.67E−02 2 59 LYD911 0.75 1.99E−02 2 30 LYD911 0.826.67E−03 2 32 LYD912 0.74 2.41E−02 1 20 LYD912 0.71 2.17E−02 3 24 LYD9130.78 2.36E−02 2 53 LYD913 0.87 1.05E−03 5 57 LYD914 0.72 1.86E−02 4 45LYD913 0.88 7.68E−04 5 65 LYD913 0.81 4.57E−03 5 66 LYD914 0.72 1.89E−025 64 LYD915 0.76 2.80E−02 2 22 LYD914 0.71 2.07E−02 4 2 LYD914 0.702.35E−02 5 67 LYD915 0.71 5.07E−02 2 46 LYD915 0.75 3.07E−02 2 25 LYD9150.81 1.40E−02 2 6 LYD915 0.72 1.78E−02 6 12 LYD917 0.77 2.56E−02 2 6LYD917 0.77 8.86E−03 4 2 LYD917 0.80 5.64E−03 4 5 LYD917 0.77 8.74E−03 47 LYD918 0.83 9.98E−03 2 59 LYD918 0.70 3.57E−02 2 20 LYD918 0.761.75E−02 2 28 LYD918 0.80 1.62E−02 2 61 LYD918 0.89 6.15E−04 5 35 LYD9190.75 3.36E−02 2 3 LYD921 0.72 4.55E−02 2 22 LYD921 0.78 2.23E−02 2 25LYD922 0.88 1.72E−03 2 30 LYD922 0.78 1.34E−02 2 32 LYD922 0.77 1.42E−021 32 LYD922 0.80 9.23E−03 1 30 LYD922 0.71 2.23E−02 5 35 LYD923 0.721.85E−02 2 47 LYD923 0.72 1.87E−02 6 12 LYD923 0.77 9.81E−03 6 9 LYD9240.80 5.50E−03 3 7 LYD924 0.71 4.79E−02 2 46 LYD924 0.74 1.53E−02 3 2LYD924 0.78 8.34E−03 3 5 LYD924 0.76 2.93E−02 2 53 LYD924 0.78 7.44E−036 65 LYD924 0.80 5.55E−03 6 66 LYD924 0.78 7.83E−03 6 57 LYD924 0.731.68E−02 4 48 LYD924 0.74 1.47E−02 4 44 LYD925 0.97 2.60E−06 5 65 LYD9250.95 3.34E−05 5 66 LYD925 0.97 5.17E−06 5 57 Table 142. Provided are thecorrelations (R) between the expression levels yield improving genes andtheir homologs in various tissues [Expression (Exp) sets] and thephenotypic performance [yield, biomass, growth rate and/or vigorcomponents (Correlation vector (Corr.))] under normal conditions acrosstomato ecotypes. P = p value.

Example 18 Production of Cotton Transcriptome and High ThroughputCorrelation Analysis with Yield and ABST Related Parameters Using 60KCotton Oligonucleotide Micro-Arrays

In order to produce a high throughput correlation analysis between plantphenotype and gene expression level, the present inventors utilized acotton oligonucleotide micro-array, produced by Agilent Technologies[chem. (dot) agilent (dot) com/Scripts/PDS (dot) asp?1Page=50879]. Thearray oligonucleotide represents about 60,000 cotton genes andtranscripts. In order to define correlations between the levels of RNAexpression with ABST and yield and components or vigor relatedparameters, various plant characteristics of 13 different cottonecotypes were analyzed and further used for RNA expression analysis. Thecorrelation between the RNA levels and the characterized parameters wasanalyzed using Pearson correlation test [davidmlane (dot)com/hyperstat/A34739 (dot) html].

Correlation of Cotton Varieties Across Ecotypes Grown Under RegularGrowth Conditions

Experimental Procedures

13 Cotton ecotypes were grown in 5-11 repetitive plots, in field.Briefly, the growing protocol was as follows: cotton plants were grownin the field using commercial fertilization and irrigation protocols[580,000 liter water per dunam (1000 square meters) per entire growthperiod, and fertilization of 24 units of nitrogen, 12 units ofphosphorous (P₂O₅) and 12 units of potassium (K₂O) per entire growthperiod; Plot size of 5 meter long, two rows, 8 plants per meter].

It should be noted that one unit of phosphorous refers to one kg of P₂O₅per dunam; and that one unit of potassium refers to one kg of K₂O perdunam;

Analyzed Cotton tissues—Six tissues [mature leaf, lower and upper mainstem, flower, main mature boll and fruit] from plants growing undernormal conditions were sampled and RNA was extracted as described above.Each micro-array expression information tissue type has received a SetID as summarized in Table 143 below.

TABLE 143 Sorghum transcriptome expression sets Set Expression Set IDMature leaf at reproductive stage under normal conditions 1 Lower mainstem at reproductive stage under normal growth 2 conditions Upper mainstem at reproductive stage under normal growth 3 conditions Main flowerat reproductive stage under normal growth conditions 4 Fruit at 10 DPAat reproductive stage under normal growth conditions 5 Main mature bollat reproductive stage under normal growth 6 conditions Table 143:Provided are the cotton transcriptome expression sets. Flag leaf = Fullexpanded leaf in the upper canopy; Lower main stem = the main stemadjacent to main mature boll, Upper main stem = the main stem adjacentto the main flower, Main flower = reproductive organ on the thirdposition on the main stem (position 3), Fruit at 10DPA = reproductiveorgan ten days after anthesis on the main stem (position 2), Main matureboll = reproductive organ on the first position on the main stem(position 1).

Cotton yield components and vigor related parameters assessment—13Cotton ecotypes in 5-11 repetitive plots, each plot containingapproximately 80 plants were grown in field. Plants were regularlyfertilized and watered during plant growth until harvesting (asrecommended for commercial growth). Plants were continuously phenotypedduring the growth period and at harvest (Table 144). The image analysissystem included a personal desktop computer (Intel P4 3.0 GHz processor)and a public domain program—ImageJ 1.37 (Java based image processingprogram, which was developed at the U.S. National Institutes of Healthand freely available on the internet [rsbweb (dot) nih (dot) gov/].Next, analyzed data was saved to text files and processed using the JMPstatistical analysis software (SAS institute).

The following parameters were measured and collected:

% Canopy coverage (10 DPA), (F)—percent Canopy coverage 10 days postanthesis (DPA) and at flowering stage. The % Canopy coverage iscalculated using Formula XXXII above.

Leaf area (10 DPA) [cm²]—Total green leaves area 10 days post anthesis.

Leaf mass fraction (10 DPA) [cm²/g]—leaf mass fraction 10 days postanthesis.

The leaf mass fraction is calculated using Formula XXXIII above.

SPAD—Plants were characterized for SPAD rate during growing period at 2time points (pre-flowering and 17 days post anthesis). Chlorophyllcontent was determined using a Minolta SPAD 502 chlorophyll meter andmeasurement was performed 64 days post sowing. SPAD meter readings weredone on young fully developed leaf. Four measurements per leaf weretaken per plot.

PAR_LAI (10DPA)—Photosynthetically active radiation 10 days postanthesis.

Shoot FW and DW [gr]—Shoot fresh weight and shoot dry weight atvegetative stage and 10 days post anthesis, after drying at 70° C. inoven for 48 hours. Total weight of 3 plants in a plot.

Plant height (H)[cm]—plants were measured for their height at harvestusing a measuring tape. Height of main stem was measured from ground toapical meristem base. Average of eight plants per plot.

Lower stem width (H)[mm]—This parameter was measured at harvest. Lowerinternodes from 8 plants per plot were separated from the plant and thediameter was measured using a caliber. The average internode width perplant was calculated by dividing the total stem width by the number ofplants.

Upper stem width (H)[mm]—This parameter was measured at harvest. Upperinternodes from 8 plants per plot were separated from the plant and thediameter was measured using a caliber. The average internode width perplant was calculated by dividing the total stem width by the number ofplants.

Relative growth rate: the relative growth rate (RGR) of Plant Height(Formula III above) RGR of SPAD (Formula IV) as described above.

Reproductive period duration—number of days from flowering to harvestfor each plot.

Number of lateral branches with open bolls (H)—count of number oflateral branches with open bolls at harvest, average of eight plants perplot.

Number of nodes with open bolls (MS) (H)—count of number of nodes withopen bolls on main stem at harvest, average of eight plants per plot.

Closed Bolls number per plant (SP)—Average closed bolls number per plantfrom selected plants.

Closed Bolls number per plant (RP)—Average closed bolls number per plantfrom the rest of the plot.

Open bolls number per plant (SP)—Average open bolls number per plantfrom selected plants. average of eight plants per plot.

Bolls number per plant (RP)—Average bolls number per plant from the restof the plot.

Bolls number in position 1 and position 3—Average bolls number from thefirst fruit node at position 1 and position 3 divided by plant number,25 days post anthesis.

Total Bolls yield (SP)[gr]—Bolls fresh weight at harvest of selectedplant.

Calculated Avr Bolls FW (MB) pO_1 and po_3 (H)[gr]—Calculated averagebolls fresh weight on main branch at positions 1 (po_1) and 3 (po_3).

Calculated Avr Fiber yield (MB) po_1 and po_3 (H) [gr]—Weight of thefiber on the main branch in position 1 and position 3 at harvest.

Fiber yield per boll (RP)[gr]—Total fiber weight in plot divided by thenumber of bolls.

Fiber yield per plant (RP)[gr] —Total fiber weight in plot divided bythe number of plants.

Fiber Length (RP)—Measure Fiber Length in inch from the rest of theplot.

Fiber Length Position 3 (SP)—Fiber length at position 3 from theselected plants. Measure Fiber Length in inch.

Fiber Length Position 1 (SP)—Fiber length at position 1 from theselected plants. Measure Fiber Length in inch.

Fiber Strength (RP)—Fiber Strength from the rest of the plot, measuredin grams per denier.

Fiber Strength Position 3 (SP)—Fiber strength at position 3 from theselected plants, measured in grams per denier.

Fiber Strength Position 1 (SP)—Fiber strength at position 1 from theselected plants. Measured in grams per denier.

Micronaire (RP)—fiber fineness and maturity from the rest of the plot.The scale that was used was 3.7-4.2—for Premium; 4.3-4.9—Base Range;above 5—Discount Range.

Micronaire Position 3 (SP)—fiber fineness and maturity from position 3from the selected plants. The scale that was used was 3.7-4.2—forPremium; 4.3-4.9—Base Range; above 5-Discount Range.

Micronaire Position 1 (SP)—fiber fineness and maturity from position 1from the selected plants. The scale that was used was 3.7-4.2—forPremium; 4.3-4.9—Base Range; above 5—Discount Range.

1000 seed weight [gr]—At the end of the experiment all seeds from allplots were collected and weighted and the weight of 1000 seeds wascalculated.

Seeds yield per plant (RP) [gr]—Total weight of seeds in plot divided inplants number.

Calculated Avr Seeds number (MB) po_l/po_3 (H)—Calculated Average Seedsnumber on main stem at position 1 and position 3 at harvest.

Calculated Avr Seeds yield (MB) po_l/po_3 (H)[gr]—Calculated Average

Seeds yield on main stem at position 1 and position 3 at harvest.

Experimental Results

13 different cotton varieties were grown and characterized for differentparameters: The average for each of the measured parameter wascalculated using the JMP software (Tables 145-146) and a subsequentcorrelation analysis between the various transcriptome sets (Table 143)and the average parameters, was conducted (Table 147). Results were thenintegrated to the database.

TABLE 144 Cotton correlated parameters (vectors) Correlated parameterwith Correlation ID % Canopy coverage (10DPA) 1 1000 seeds weight (RP)[gr] 2 Bolls num per plant (RP) 3 Closed Bolls num per plant (RP) 4Closed Bolls num per plant (SP) 5 Fiber Length (RP) 6 Fiber LengthPosition 3 (SP) 7 Fiber Strength (RP) 8 Fiber Strength Position 3 (SP) 9Fiber yield per boll (RP) [gr] 10 Fiber yield per plant (RP) [gr] 11Leaf area (10DPA) [cm²] 12 Lower Stem width (H) [mm] 13 Micronaire (RP)14 Micronaire Position 3 (SP) 15 Num of lateral branches with open bolls(H) 16 Num of nodes with open bolls (MS) (H) 17 Open Bolls num per plant(SP) 18 PAR_LAI (10 DPA) 19 Plant height (H) [cm] 20 Plant height growth21 Reproductive period duration 22 SPAD (17 DPA) 23 SPAD (pre F) 24 SPADrate 25 Seeds yield per plant (RP) [gr] 26 Shoot DW (10 DPA) [gr] 27Shoot DW (V) [gr] 28 Shoot FW (10 DPA) [gr] 29 Shoot FW (V) [gr] 30Total Bolls yield (SP) [gr] 31 Upper Stem width (H) [mm] 32 bolls num inposition 1 33 bolls num in position 3 34 estimated Avr Bolls FW (MB)po_1 (H) [gr] 35 estimated Avr Bolls FW (MB) po_3 (H) [gr] 36 estimatedAvr Fiber yield (MB) po_1 (H) [gr] 37 estimated Avr Fiber yield (MB)po_3 (H) [gr] 38 estimated Avr Seeds num (MB) po_1 (H) 39 estimated AvrSeeds num (MB) po_3 (H) 40 estimated Avr Seeds yield (MB) po_1 (H) [gr]41 estimated Avr Seeds yield (MB) po_3 (H) [gr] 42 leaf mass fraction(10DPA) [cm²/g] 43 Table 144. Provided are the Cotton correlatedparameters (vectors). “gr.” = grams; “SPAD” = chlorophyll levels; “FW” =Plant Fresh weight; “normal” = standard growth conditions.

TABLE 145 Measured parameters in Cotton accessions (1-7) Ecotype/Treatment Line-1 Line-2 Line-3 Line-4 Line-5 Line-6 Line-7 1 84.01 94.8692.93 89.23 84.88 87.15 79.89 2 105.24 113.64 98.49 84.74 111.74 82.4791.64 3 11.01 19.11 11.83 15.49 22.62 11.78 13.45 4 4.23 NA NA NA NA NA4.56 5 5.55 2.08 3.39 2.09 3.07 2.41 5.89 6 1.16 1.28 1.15 1.12 1.411.07 0.90 7 1.15 1.30 1.14 1.10 1.44 0.96 0.84 8 28.80 34.47 25.88 29.2039.66 22.60 22.58 9 29.60 36.55 26.17 29.63 39.53 20.10 21.57 10 2.301.37 2.22 1.81 1.12 0.40 1.80 11 25.18 26.00 25.37 27.87 25.35 4.6724.02 12 7007.67 6622.34 5544.74 8196.02 8573.30 8155.29 5291.27 1312.79 13.71 11.83 12.38 12.97 10.92 12.97 14 4.31 3.63 3.95 4.37 4.106.05 5.01 15 4.57 3.89 3.99 4.71 4.75 5.69 5.25 16 1.02 1.46 0.81 0.961.21 1.69 1.29 17 8.15 10.90 9.00 11.04 10.14 7.85 8.48 18 11.98 22.5611.80 18.75 27.65 16.42 15.00 19 5.67 6.87 6.45 5.86 5.61 6.59 4.09 20112.80 110.77 100.59 115.45 103.26 98.52 121.91 21 1.86 2.00 1.73 1.721.66 1.72 2.09 22 121.33 108.11 108.00 103.80 102.88 108.00 126.00 2334.29 33.52 31.41 29.66 37.10 27.43 33.39 24 32.13 35.30 35.99 35.8035.03 32.92 35.89 25 0.04 −0.06 −0.26 −0.22 0.10 −0.29 −0.14 26 32.4934.86 32.48 35.06 36.32 26.74 33.06 27 169.15 183.58 171.09 172.70190.03 149.03 193.14 28 39.20 64.68 44.79 38.06 46.23 36.68 48.20 29842.47 792.64 804.23 766.97 745.20 725.93 922.57 30 168.94 256.04 194.76155.69 154.56 172.13 193.28 31 505.37 564.21 544.17 585.47 536.54 317.18488.33 32 3.02 3.64 3.32 3.13 3.23 2.73 2.80 33 5.00 5.00 5.00 5.00 5.005.00 5.00 34 5.00 5.00 5.00 5.00 5.00 5.00 5.00 35 6.62 4.88 7.08 5.344.08 3.58 5.66 36 6.42 2.93 5.95 4.16 2.72 2.73 5.13 37 2.53 1.88 2.692.02 1.50 0.38 2.04 38 2.46 1.13 2.34 1.69 1.06 0.50 1.87 39 31.56 24.1636.01 31.31 20.94 32.59 30.77 40 31.23 15.50 33.29 26.13 14.87 31.2532.63 41 3.33 2.70 3.83 2.99 2.43 3.02 3.03 42 3.29 1.58 3.06 2.19 1.642.29 2.76 43 41.10 36.48 33.99 47.95 44.56 54.74 28.14 Table 145.Provided are the values of each of the parameters (as described above)measured in Cotton accessions (ecotype) under normal conditions. Growthconditions are specified in the experimental procedure section.

TABLE 146 Additional measured parameters in Cotton accessions (8-13)Ecotype/ Treatment Line-8 Line-9 Line-10 Line-11 Line-12 Line-13 1 85.1983.55 84.53 95.90 95.92 83.89 2 116.68 99.58 99.55 97.72 102.72 109.95 321.94 13.92 11.56 17.33 14.98 12.15 4 NA NA 3.16 1.11 NA NA 5 2.34 3.753.31 1.84 2.74 3.09 6 1.38 1.18 1.12 1.12 1.18 1.18 7 1.41 1.14 1.071.11 1.20 1.20 8 42.63 28.87 25.87 28.98 30.82 29.77 9 42.70 28.38 23.6730.30 31.97 30.53 10 1.24 2.23 1.99 1.18 1.74 2.39 11 26.64 30.80 23.1420.49 25.97 29.14 12 8854.54 5650.67 6003.34 6691.84 9004.97 7268.00 1313.07 14.26 11.84 14.48 12.57 14.00 14 3.88 3.98 4.10 4.55 4.76 4.93 154.48 4.19 4.51 4.21 4.25 4.74 16 1.13 0.80 0.58 0.13 0.15 0.71 17 11.2910.83 8.73 12.33 9.19 10.65 18 30.29 17.90 12.40 19.56 14.67 15.67 195.63 5.62 5.33 7.41 7.54 5.51 20 102.22 127.29 105.85 151.27 117.64119.24 21 1.63 2.07 1.86 1.57 1.87 1.94 22 102.71 104.36 126.00 145.17109.50 106.17 23 33.79 31.91 32.87 22.08 28.07 31.13 24 33.63 35.2638.12 32.77 34.44 35.33 25 −0.08 −0.13 −0.24 −0.51 −0.24 −0.24 26 39.5439.68 30.15 47.61 37.79 35.85 27 196.45 199.76 179.43 134.30 198.46165.53 28 50.81 51.71 39.70 35.34 42.12 42.05 29 802.23 861.63 930.97591.63 911.42 791.81 30 230.40 176.68 176.53 163.68 164.66 170.94 31620.54 715.10 421.32 531.77 405.27 715.72 32 2.99 3.45 2.88 3.40 3.283.29 33 5.00 5.00 5.00 NA 5.00 5.00 34 5.00 5.00 5.00 5.00 5.00 5.00 353.13 6.37 6.14 NA 4.95 6.95 36 3.31 4.71 5.44 4.14 4.60 6.25 37 1.142.47 2.29 NA 1.77 2.92 38 1.19 1.91 2.02 1.12 1.65 2.65 39 15.45 31.4529.29 NA 25.62 34.56 40 18.21 25.13 28.98 29.15 25.92 32.67 41 1.87 3.213.00 NA 2.82 3.87 42 2.06 2.25 2.65 2.73 2.55 3.56 43 45.41 28.05 33.4847.94 45.95 44.01 Provided are the values of each of the parameters (asdescribed above) measured in Cotton accessions (ecotype) under normalconditions. Growth conditions are specified in the experimentalprocedure section.

TABLE 147 Correlation between the expression level of selected genes ofsome embodiments of the invention in various tissues and the phenotypicperformance under normal conditions across Cotton accessions Gene Exp.Corr. Gene Exp. Corr. Name R P value set Set ID Name R P value set SetID LGP47 0.81 2.69E−02 2 32 LGP47 0.72 6.94E−02 2 19 LGP47 0.72 7.83E−034 18 LYD838 0.73 6.08E−02 2 32 LGP47 0.92 3.56E−03 1 42 LYD841 0.801.99E−03 6 37 LGP47 0.99 1.97E−05 1 14 LYD843 0.75 3.02E−03 6 7 LGP470.74 8.97E−02 1 39 LYD843 0.81 8.32E−04 6 8 LGP47 0.78 3.70E−02 1 36LYD843 0.77 1.90E−03 6 6 LGP47 0.84 1.80E−02 2 1 LYD850 0.99 8.98E−06 125 LGP47 0.72 8.12E−03 4 6 LYD850 0.87 2.40E−04 3 28 LGP58 0.70 7.84E−022 43 LYD843 0.74 6.27E−03 4 9 LGP58 0.71 9.10E−03 3 12 LYD849 0.832.06E−02 1 38 LGP58 0.71 6.90E−03 6 15 LYD845 0.71 7.52E−02 1 27 LGP650.83 2.69E−03 5 43 LGP65 0.85 1.65E−03 5 14 LGP65 0.70 1.06E−02 4 7LYD841 0.73 6.18E−02 2 32 LGP65 0.81 1.37E−03 4 8 LYD843 0.71 7.17E−02 243 LGP65 0.74 5.88E−02 1 38 LYD844 0.76 4.13E−03 6 39 LGP65 0.824.61E−02 1 35 LYD847 0.79 2.01E−03 6 35 LGP65 0.83 3.94E−02 1 37 LYD8490.79 1.45E−03 6 10 LGP65 0.78 3.87E−02 2 22 LYD850 0.77 4.12E−02 1 6LGP65 0.75 4.92E−03 4 9 LYD837 0.74 5.67E−03 3 3 LYD835 0.77 4.48E−02 142 LYD849 0.77 3.60E−03 6 37 LYD835 0.77 4.48E−02 1 40 LYD842 0.716.52E−03 6 38 LYD835 0.75 4.99E−02 2 30 LGP65 0.86 1.22E−02 1 21 LYD8360.73 1.74E−02 5 43 LYD836 0.80 5.25E−03 5 14 LYD836 0.85 1.43E−02 1 42LGP47 0.74 9.48E−02 1 35 LYD836 0.72 6.81E−02 1 14 LGP47 0.85 1.57E−02 140 LYD836 0.93 7.69E−03 1 39 LGP47 0.78 7.02E−02 1 37 LYD836 0.793.48E−02 1 36 LGP47 0.79 6.19E−02 1 41 LYD836 0.74 8.66E−03 3 39 LYD8490.83 4.00E−02 1 35 LYD836 0.73 7.59E−03 4 1 LYD843 0.72 7.88E−03 3 30LYD837 0.78 3.76E−02 2 2 LYD837 0.70 7.80E−02 2 6 LYD837 0.78 2.58E−03 39 LYD849 0.78 6.82E−02 1 37 LYD837 0.90 5.68E−03 1 32 LYD838 0.701.13E−02 3 28 LYD838 0.77 4.31E−02 2 19 LYD838 0.89 7.87E−03 2 1 LYD8380.72 5.60E−03 6 18 LYD849 0.81 1.41E−03 4 8 LYD838 0.73 5.04E−03 6 3LYD849 0.72 7.88E−03 4 9 LYD838 0.74 5.88E−02 1 7 LGP65 0.79 3.36E−02 110 LYD838 0.79 3.62E−02 1 8 LGP65 0.82 4.64E−02 1 39 LYD838 0.755.36E−02 1 6 LGP65 0.79 6.21E−02 1 41 LYD839 0.72 6.59E−02 2 30 LYD8390.74 5.75E−02 2 6 LYD839 0.77 8.62E−03 5 14 LYD849 0.74 5.65E−02 1 5LYD840 0.88 1.92E−04 4 42 LYD844 0.84 1.84E−02 2 40 LYD840 0.80 1.65E−034 40 LYD850 0.78 3.91E−02 2 7 LYD840 0.72 8.20E−03 4 36 LGP47 0.727.78E−03 4 8 LYD841 0.80 5.56E−03 5 38 LYD841 0.84 2.57E−03 5 10 LYD8410.84 4.25E−03 5 35 LYD841 0.83 5.11E−03 5 37 LYD841 0.93 2.51E−03 2 20LYD841 0.75 5.45E−02 2 11 LYD841 0.71 6.39E−03 6 38 LYD836 0.70 1.12E−024 19 LYD841 0.75 4.83E−03 6 35 LYD840 0.83 7.70E−04 4 22 LYD841 0.751.22E−02 5 36 LYD850 0.84 1.71E−02 1 16 LYD841 0.71 1.04E−02 4 8 LYD8470.80 1.93E−03 3 10 LYD842 0.71 9.18E−03 3 22 LYD849 0.81 2.79E−02 1 36LYD842 0.71 6.21E−03 6 36 LGP58 0.71 7.26E−02 1 43 LYD842 0.82 2.52E−021 20 LYD843 0.80 1.81E−03 3 18 LYD843 0.95 8.97E−04 2 14 LYD843 0.861.35E−02 2 15 LYD843 0.73 6.61E−03 4 7 LGP65 0.72 8.29E−03 4 18 LYD8430.81 1.47E−03 4 8 LGP65 0.71 9.91E−03 4 6 LYD843 0.76 3.81E−03 4 6LYD840 0.73 1.05E−02 4 35 LYD843 0.70 7.46E−03 6 2 LYD844 0.71 1.04E−024 42 LYD843 0.79 1.36E−03 6 18 LGP58 0.72 5.32E−03 6 14 LYD843 0.818.53E−04 6 3 LYD847 0.79 1.18E−03 6 38 LYD843 0.71 7.39E−02 1 18 LYD8350.88 8.12E−03 1 14 LYD843 0.75 5.44E−02 1 31 LYD835 0.80 3.11E−02 1 20LYD843 0.78 1.52E−03 6 9 LYD836 0.87 1.16E−02 1 22 LYD843 0.73 6.28E−021 13 LYD844 0.75 4.72E−03 3 40 LYD843 0.81 1.48E−03 3 3 LYD844 0.769.99E−03 5 38 LYD844 0.71 2.16E−02 5 21 LYD844 0.71 2.12E−02 5 10 LYD8440.84 2.28E−03 5 42 LYD844 0.75 1.29E−02 5 40 LYD844 0.78 1.30E−02 5 35LYD844 0.77 1.51E−02 5 41 LYD844 0.89 6.54E−04 5 36 LYD844 0.75 1.21E−025 5 LYD844 0.79 6.12E−02 1 41 LYD844 0.71 7.38E−02 2 41 LYD844 0.896.53E−03 2 39 LYD840 0.73 1.06E−02 4 39 LYD844 0.71 1.34E−02 4 35 LYD8400.84 1.14E−03 4 41 LYD844 0.72 1.31E−02 4 39 LYD849 0.83 4.72E−04 6 38LYD844 0.71 6.46E−03 6 40 LYD836 0.96 2.99E−03 1 35 LYD844 0.74 5.91E−021 42 LYD836 0.95 1.02E−03 1 40 LYD844 0.85 1.54E−02 1 40 LYD836 0.928.24E−03 1 37 LYD844 0.86 2.66E−02 1 37 LYD850 0.77 4.35E−02 1 18 LYD8440.76 6.57E−03 3 39 LYD845 0.79 3.29E−02 2 15 LYD845 0.84 1.70E−02 2 16LYD837 0.73 6.33E−02 1 28 LYD845 0.78 1.86E−03 6 30 LGP47 0.70 1.08E−023 21 LYD845 0.84 2.09E−03 5 14 LYD846 0.72 2.01E−02 5 15 LYD846 0.717.27E−02 1 15 LYD847 0.79 1.22E−02 5 41 LYD847 0.85 4.06E−03 5 39 LYD8470.94 1.41E−03 2 5 LYD847 0.80 2.98E−02 2 22 LYD847 0.71 7.62E−02 2 24LYD847 0.83 2.16E−02 2 21 LYD847 0.81 2.80E−02 2 29 LYD847 0.71 7.33E−022 10 LYD844 0.81 1.54E−03 4 26 LYD847 0.72 6.67E−02 2 36 LYD838 0.716.78E−03 6 8 LYD847 0.80 9.62E−04 6 10 LYD836 0.86 2.67E−02 1 41 LYD8470.77 4.28E−02 1 22 LYD838 0.91 3.90E−03 1 18 LYD847 0.72 6.58E−02 1 20LYD842 0.96 7.51E−04 1 22 LYD847 0.82 1.10E−03 6 37 LYD847 0.79 3.77E−033 37 LYD847 0.86 3.87E−04 3 38 LYD847 0.90 1.51E−04 3 41 LYD847 0.901.64E−04 3 35 MGP1 0.73 6.50E−03 4 22 LYD847 0.95 1.11E−05 3 39 LYD8370.82 9.97E−04 3 8 LYD847 0.84 5.58E−04 3 36 LYD838 0.97 3.74E−04 1 3LYD848 0.77 4.08E−02 1 22 LYD838 0.80 3.18E−02 1 9 LYD848 0.85 1.56E−021 17 LYD849 0.79 6.44E−03 5 42 LYD849 0.83 2.71E−03 5 38 LYD849 0.752.08E−02 5 35 LYD849 0.75 1.17E−02 5 10 LYD849 0.82 3.33E−03 5 36 LYD8490.75 1.97E−02 5 37 LYD849 0.80 2.92E−02 2 42 LYD849 0.97 3.35E−04 2 38LYD849 0.71 7.36E−02 2 32 LYD849 0.95 1.28E−03 2 10 LYD849 0.94 1.57E−032 37 LYD849 0.81 2.62E−02 2 35 LYD849 0.79 3.59E−02 2 11 LYD849 0.717.35E−02 2 13 LYD843 0.84 6.44E−04 4 18 LYD849 0.84 7.16E−04 4 18 LYD8430.85 4.99E−04 4 3 LYD849 0.74 5.74E−03 4 3 LYD844 0.77 3.40E−03 4 17LYD849 0.93 2.47E−03 2 36 LYD838 0.71 6.59E−03 6 6 LYD849 0.77 1.99E−036 42 LYD841 0.75 2.98E−03 6 10 LYD849 0.76 3.76E−03 6 35 LYD843 0.793.55E−02 1 14 LYD849 0.73 6.51E−02 1 21 LYD843 0.89 7.67E−03 1 17 LYD8490.88 8.24E−03 1 10 LYD844 0.90 1.48E−02 1 35 LYD849 0.78 6.57E−02 1 39LYD844 0.86 2.78E−02 1 39 LYD849 0.71 7.38E−02 1 29 LYD850 0.80 3.09E−021 8 LYD849 0.73 7.29E−03 3 24 LYD844 0.85 1.51E−02 1 22 LYD849 0.817.63E−04 6 36 LYD836 0.74 5.50E−03 3 40 LYD849 0.73 2.46E−02 5 41 LYD8500.70 7.96E−02 2 28 LYD850 0.87 1.18E−02 2 18 LYD850 0.82 2.29E−02 2 32LYD850 0.89 7.44E−03 2 8 LYD850 0.70 7.98E−02 2 27 LYD850 0.93 2.60E−032 3 LYD850 0.87 9.98E−03 2 6 LYD850 0.85 1.62E−02 2 25 LYD844 0.764.64E−02 1 20 LYD850 0.74 5.94E−02 1 7 LYD847 0.81 2.60E−02 1 19 LYD8500.93 2.63E−03 1 23 LYD847 0.74 5.54E−02 1 1 LYD850 0.86 1.21E−02 1 12LYD848 0.77 4.19E−02 1 32 LYD850 0.74 5.50E−02 1 27 LYD848 0.73 6.43E−021 13 LYD850 0.79 3.35E−02 1 15 LYD850 0.72 6.60E−02 1 3 LYD850 0.763.97E−03 3 30 LYD840 0.73 6.47E−02 1 14 LYD850 0.83 2.05E−02 2 9 LYD8370.81 1.26E−03 3 18 LYD850 0.76 1.16E−02 5 13 LYD847 0.75 5.28E−03 3 40MGP1 0.73 1.55E−02 5 13 Provided are the correlations (R) between theexpression levels of yield improving genes and their homologues intissues [mature leaf, lower and upper main stem, flower, main matureboll and fruit; Expression sets (Exp)] and the phenotypic performance invarious yield, biomass, growth rate and/or vigor components [Correlationvector (corr.)] under normal conditions across Cotton accessions. P = pvalue.

Example 19 Production of Bean Transcriptome and High ThroughputCorrelation Analysis with Yield Parameters Using 60K Bean (Phaseolusvulgaris L.) Oligonucleotide Micro-Arrays

In order to produce a high throughput correlation analysis, the presentinventors utilized a Bean oligonucleotide micro-array, produced byAgilent Technologies [chem. (dot) agilent (dot) com/Scripts/PDS (dot)asp?1Page=50879]. The array oligonucleotide represents about 60,000 Beangenes and transcripts. In order to define correlations between thelevels of RNA expression with yield components or plant architecturerelated parameters or plant vigor related parameters, various plantcharacteristics of 40 different commercialized bean varieties wereanalyzed and further used for RNA expression analysis. The correlationbetween the RNA levels and the characterized parameters was analyzedusing Pearson correlation test [davidmlane (dot) com/hyperstat/A34739(dot) html].

Experimental Procedures

Analyzed Bean Tissues

Six tissues [leaf, Stem, lateral stem, lateral branch flower bud,lateral branch pod with seeds and meristem] growing under normalconditions [field experiment, normal growth conditions which includedirrigation with water 2-3 times a week with 524 m³ water per dunam (1000square meters) per entire growth period, and fertilization of 16 unitsnitrogen per dunam given in the first month of the growth period] weresampled and RNA was extracted as described above.

For convenience, each micro-array expression information tissue type hasreceived a Set ID as summarized in Table 148 below.

TABLE 148 Bean transcriptome expression sets Expression Set Set IDLateral branch flower bud at flowering stage under normal 1 growthconditions Lateral branch pod with seeds at pod setting stage undernormal 2 growth conditions Lateral stem at pod setting stage undernormal growth conditions 3 Lateral stem at flowering stage under normalgrowth conditions 4 Leaf at pod setting stage under normal growthconditions 5 Leaf at flowering stage under normal growth conditions 6Leaf at vegetative stage under normal growth conditions 7 Meristem atvegetative stage under normal growth conditions 8 stem at vegetativestage under normal growth conditions 9 Table 148: Provided are the beantranscriptome expression sets. Lateral branch flower bud = flower budfrom vegetative branch; Lateral branch pod with seeds = pod with seedsfrom vegetative branch; Lateral stem = stem from vegetative branch.

Bean Yield Components and Vigor Related Parameters Assessment

40 Bean varieties were grown in five repetitive plots, in field.Briefly, the growing protocol was as follows: Bean seeds were sown insoil and grown under normal conditions until harvest. Plants werecontinuously phenotyped during the growth period and at harvest (Table149). The image analysis system included a personal desktop computer(Intel P4 3.0 GHz processor) and a public domain program—ImageJ 1.37(Java based image processing program, which was developed at the U.S.National Institutes of Health and freely available on the internet[rsbweb (dot) nih (dot) gov/]. Next, analyzed data was saved to textfiles and processed using the JMP statistical analysis software (SASinstitute).

The collected data parameters were as follows:

% Canopy coverage—percent Canopy coverage at grain filling stage, R1flowering stage and at vegetative stage. The % Canopy coverage iscalculated using Formula XXXII above.

1000 seed weight [gr]—At the end of the experiment all seeds from allplots were collected and weighted and the weight of 1000 werecalculated.

Days till 50% flowering [days]—number of days till 50% flowering foreach plot.

Avr shoot DW—At the end of the experiment, the shoot material wascollected, measured and divided by the number of plants.

Big pods FW per plant (PS) [gr]—1 meter big pods fresh weight at podsetting divided by the number of plants.

Big pods num per plant (PS)—number of pods at development stage of R3-4period above 4 cm per plant at pod setting.

Small pods FW per plant (PS) [gr]—1 meter small pods fresh weight at podsetting divided by the number of plants.

Small pods num per plant (PS)—number of pods at development stage ofR3-4 period below 4 cm per plant at pod setting.

Pod Area [cm²]—At development stage of R3-4 period pods of three plantswere weighted, photographed and images were processed using the belowdescribed image processing system. The pod area above 4 cm and below 4cm was measured from those images and was divided by the number of pods.

Pod Length and Pod width [cm]—At development stage of R3-4 period podsof three plants were weighted, photographed and images were processedusing the below described image processing system. The sum of podlengths/or width (longest axis) was measured from those images and wasdivided by the number of pods.

Num of lateral branches per plant [value/plant]—number of lateralbranches per plant at vegetative stage (average of two plants per plot)and at harvest (average of three plants per plot).

Relative growth rate [cm/day]: the relative growth rate (RGR) of PlantHeight was calculated using Formula III above.

Leaf area per plant (PS) [cm²]=Total leaf area of 3 plants in a plot atpod setting. Measurement was performed using a Leaf area-meter.

Specific leaf area (PS) [cm²/gr]—leaf area per leaf dry weight at podset.

Leaf form—Leaf length (cm)/leaf width (cm); average of two plants perplot.

Leaf number per plant (PS)—Plants were characterized for leaf numberduring pod setting stage. Plants were measured for their leaf number bycounting all the leaves of 3 selected plants per plot.

Plant height [cm]—Plants were characterized for height during growingperiod at 3 time points. In each measure, plants were measured for theirheight using a measuring tape. Height of main stem was measured fromfirst node above ground to last node before apex.

Seed yield per area (H)[gr]—1 meter seeds weight at harvest.

Seed yield per plant (H)[gr]—Average seeds weight per plant at harvestin 1 meter plot.

Seeds num per area (H)—1 meter plot seeds number at harvest.

Total seeds per plant (H)—Seeds number on lateral branch per plant+Seedsnumber on main branch per plant at harvest, average of three plants perplot.

Total seeds weight per plant (PS)—Seeds weight on lateral branch+Seedsweight on main branch at pod set per plant, average of three plants perplot.

Small pods FW per plant (PS)—Average small pods (below 4 cm) freshweight per plant at pod setting per meter.

Small pods num per plant (PS)—Number of Pods below 4 cm per plant at podsetting, average of two plants per plot.

SPAD—Plants were characterized for SPAD rate during growing period atgrain filling stage and vegetative stage. Chlorophyll content wasdetermined using a Minolta SPAD 502 chlorophyll meter and measurementwas performed 64 days post sowing. SPAD meter readings were done onyoung fully developed leaf. Three measurements per leaf were taken perplot.

Stem width (R2F)[mm]—width of the stem of the first node at R2 floweringstage, average of two plants per plot.

Total pods num per plant (H), (PS)—Pods number on lateral branch perplant+Pods number on main branch per plant at pod setting and atharvest, average of three plants per plot.

Total pods DW per plant (H) [gr]—Pods dry weight on main branch perplant+Pods dry weight on lateral branch per plant at harvest, average ofthree plants per plot.

Total pods FW per plant (PS) [gr]—Average pods fresh weight on lateralbranch+Pods weight on main branch at pod setting.

Pods weight per plant (RP) (H) [gr]—Average pods weight per plant atharvest in 1 meter.

Total seeds per plant (H), (PS)—Seeds number on lateral branch perplant+Seeds number on main branch per plant at pod setting and atharvest. average of three plants per plot.

Total seeds num per pod (H), (PS)—Total seeds num per plant divided intotal pods num per plant, average of three plants per plot.

Vegetative FW and DW per plant (PS) [gr/plant]—total weight of thevegetative portion above ground (excluding roots and pods) before andafter drying at 70° C. in oven for 48 hours at pod set, average of threeplants per plot.

Vigor till flowering [g/day]—Relative growth rate (RGR) of shootDW=Regression coefficient of shoot DW along time course (twomeasurements at vegetative stage and one measurement at floweringstage).

Vigor post flowering [g/day]—Relative growth rate (RGR) of shootDW=Regression coefficient of shoot DW measurements along time course(one measurement at flowering stage and two measurements at grainfilling stage).

Experimental Results

40 different bean varieties lines 1-40 were grown and characterized for48 parameters as specified above. Among the 40 varieties, 16 varietiesare “fine” and “extra fine”. The average for each of the measuredparameters was calculated using the JMP software and values aresummarized in Tables 150-154 below. Subsequent correlation analysisbetween the various transcriptome sets and the average parameters wasconducted (Table 157). Follow, results were integrated to the database.Correlations were calculated across all 40 lines. The phenotypic data ofall 40 lines is provided in Tables 150-154 below. The correlation dataof all 40 lines is provided in Table 157 below. The phenotypic data of“fine” and “extra fine” lines is provided in Tables 155-156 below. Thecorrelation data of “fine” and “extra fine” lines is provided in Table158 below.

TABLE 149 Bean correlated parameters (vectors) Correlated parameter withCorrelation ID % Canopy coverage (GF) 1 % Canopy coverage (R1F) 2 %Canopy coverage (V) 3 1000 seed weight [gr] 4 Avr shoot DW (EGF) [gr] 5Avr shoot DW (R2F) [gr] 6 Avr shoot DW (V) [gr] 7 Big pods FW per plant(PS) (RP) [gr] 8 Big pods num per plant (PS) [gr] 9 CV (Pod_Length) 10CV (Pod_Length_Below_4 cm) 11 Height Rate 12 Leaf Length 13 Leaf Width14 Leaf area per plant (PS) 15 Leaf form 16 Leaf num per plant (PS) 17Num of lateral branches per plant (H) 18 Num of lateral branches perplant (V) 19 PAR_LAI (EGF) 20 PAR_LAI (LGF) 21 PAR_LAI (R1F) 22 Plantheight (GF) 23 Plant height (V2-V3) 24 Plant height (V4-V5) 25 Podsweight per plant (RP) (H) [gr] 26 SPAD (GF) 27 SPAD (V) 28 Seed yieldper area (H) (RP) [gr] 29 Seed yield per plant (RP) (H) [gr] 30 Seedsnum per area (H) (RP) 31 Small pods FW per plant (PS) (RP) [gr] 32 Smallpods num per plant (PS) 33 Specific leaf area (PS) 34 Stem width (R2F)35 Total pods DW per plant (H) [gr] 36 Total pods num per plant (H) 37Total pods num per plant (PS) 38 Total pods weight per plant (PS) [gr]39 Total seeds num per pod (H) 40 Total seeds num per pod (PS) 41 Totalseeds per plant (H) 42 Total seeds per plant (PS) 43 Total seeds weightper plant (PS) [gr] 44 Vegetative DW per plant (PS) [gr] 45 VegetativeFW per plant (PS) [gr] 46 Vigor post flowering 47 Vigor till flowering48 Table 149. Provided are the Bean correlated parameters (vectors).“gr.” = grams; “SPAD” = chlorophyll levels; “PAR” = Photosyntheticallyactive radiation; “FW” = Plant Fresh weight; “normal” = standard growthconditions; “GF” = Grain filling; “R1F” = Flowering in R1 stage; “V” =Vegetative stage; “EGF” = Early grain filling; “R2F” = Flowering in R2stage; “PS” = Pod setting; “RP” = Rest of the plot; “H” = Harvest; “LGF”= Late grain filling; “V2-V3” = Vegetative stages 2-3; “V4-V5” =Vegetative stages 4-5.

TABLE 150 Measured parameters in bean varieties (lines 1-8) Ecotype/Treatment Line-1 Line-2 Line-3 Line-4 Line-5 Line-6 Line-7 Line-8 188.66 87.35 78.24 91.02 NA 80.76 76.70 90.29 2 89.59 82.80 66.40 78.8779.25 72.28 82.77 90.49 3 70.53 61.65 56.46 58.56 65.39 38.98 70.5483.64 4 94.43 151.19 145.91 117.59 154.23 69.63 142.25 123.75 5 16.1928.63 14.04 18.66 23.18 19.29 18.43 27.82 6 7.33 10.29 7.58 8.28 9.426.37 11.51 11.85 7 0.30 0.42 0.30 0.33 0.41 0.24 0.44 0.44 8 NA NA NA67.40 NA 38.22 NA 76.45 9 24.25 36.00 25.25 35.25 19.50 65.00 28.5026.50 10 19.39 46.26 18.29 40.69 54.77 36.57 36.81 19.08 11 NA 53.11 NA48.72 47.60 38.91 41.17 67.38 12 0.97 0.90 0.85 0.85 0.76 0.91 1.33 0.8513 13.34 12.31 11.76 11.64 12.19 11.14 13.20 13.15 14 8.16 7.75 7.698.83 7.67 7.03 8.97 8.42 15 211.67 242.06 183.00 307.13 306.53 133.13253.07 308.07 16 1.64 1.59 1.53 1.32 1.59 1.58 1.47 1.56 17 4.73 4.674.67 6.07 5.00 4.73 5.00 6.17 18 7.93 6.06 7.00 6.20 7.27 7.93 6.93 7.0019 4.90 5.17 5.50 4.90 5.30 5.80 6.60 6.60 20 8.44 6.39 4.85 7.85 6.105.78 7.82 7.61 21 6.15 4.76 3.97 5.84 NA 4.38 4.03 4.01 22 3.27 3.432.05 3.06 3.21 1.33 4.11 5.01 23 36.84 31.98 30.76 34.83 34.37 31.5251.66 37.71 24 4.39 5.81 4.53 4.80 5.19 3.68 6.41 5.75 25 11.43 10.578.33 11.17 14.79 7.60 17.50 16.57 26 11.67 20.34 15.07 15.20 20.20 15.9614.36 23.07 27 40.19 38.43 34.50 36.22 38.60 37.68 40.53 NA 28 36.0040.03 30.82 39.44 33.66 31.41 35.44 40.15 29 342.44 243.25 284.35 457.16493.65 196.69 457.67 430.61 30 6.31 4.73 8.70 8.29 9.28 4.53 8.40 9.2031 3635.20 1588.67 1958.33 3879.60 3207.60 2875.20 3218.20 3485.80 320.62 2.16 1.52 2.06 0.72 1.15 0.87 0.60 33 0.50 3.75 0.25 6.00 4.75 9.501.75 1.50 34 226.25 226.14 211.39 222.25 207.28 213.00 200.97 207.31 355.79 5.65 6.14 5.84 6.01 5.40 6.10 5.83 36 12.76 15.64 15.42 20.71 16.5413.89 19.23 30.42 37 27.13 19.35 17.56 24.73 17.93 46.07 18.53 38.27 3833.07 24.67 29.67 33.93 16.80 31.58 27.50 20.94 39 32.96 122.68 60.41105.04 40.17 61.14 50.37 33.15 40 3.32 3.32 3.92 4.68 3.94 2.81 4.463.93 41 2.64 2.22 3.94 2.35 4.13 1.02 3.66 0.63 42 90.47 64.18 70.22111.33 67.67 128.60 81.00 151.80 43 87.60 51.87 117.20 79.00 68.87 29.3892.60 9.17 44 NA NA NA 3.45 NA 0.50 NA 0.17 45 16.30 NA 14.80 13.5311.36 18.80 16.38 12.64 46 91.61 62.45 81.49 65.65 64.54 61.83 85.7771.07 47 0.92 1.26 1.04 2.03 1.97 1.67 0.87 0.84 48 0.44 0.61 0.27 0.460.52 0.35 1.10 1.18

TABLE 151 Measured parameters in bean varieties (lines 9-16) Ecotype/Line- Line- Line- Line- Line- Treatment Line-9 Line-10 Line-11 12 13 1415 16 1 82.43 70.03 84.86 70.84 78.11 84.27 NA NA 2 76.92 76.66 85.9382.06 77.77 73.78 76.45 71.73 3 69.36 68.78 53.71 64.00 71.82 46.9151.88 61.04 4 149.23 191.85 124.61 151.53 149.49 66.31 93.68 147.99 515.82 31.36 26.38 24.74 20.06 14.44 18.02 22.65 6 9.34 10.13 8.74 8.669.26 5.42 7.40 13.47 7 0.38 0.44 0.33 0.39 0.34 0.21 0.35 0.48 8 NA NANA NA NA 49.40 43.69 71.54 9 39.25 33.25 31.00 28.25 35.25 38.75 35.5028.00 10 43.94 51.86 29.45 35.20 38.96 17.38 41.36 46.35 11 46.79 42.6730.14 37.78 33.11 41.28 55.89 42.56 12 1.12 0.84 0.83 0.87 0.94 0.721.06 0.83 13 12.22 12.20 12.13 12.21 12.34 11.99 12.35 13.95 14 8.338.72 7.83 8.10 8.51 7.85 8.13 8.84 15 161.62 193.33 145.57 204.86 194.50157.53 155.00 194.42 16 1.46 1.40 1.55 1.51 1.45 1.53 1.52 1.58 17 3.214.47 4.00 4.20 4.73 5.00 5.42 4.11 18 7.60 7.60 5.73 6.47 6.87 9.67 7.537.58 19 4.80 6.50 4.90 4.80 5.70 5.10 5.70 6.75 20 6.20 4.58 6.34 6.796.48 6.29 6.60 5.85 21 4.20 2.58 4.66 3.69 3.40 4.95 NA NA 22 4.26 2.882.22 2.99 2.84 1.58 1.74 2.73 23 43.67 34.58 32.94 38.28 37.63 28.8839.83 32.98 24 6.25 7.10 5.16 5.95 5.94 3.93 4.50 5.85 25 14.07 14.3710.37 13.20 12.07 8.40 9.67 11.17 26 14.94 17.78 13.45 11.85 14.54 17.0615.12 20.37 27 43.58 NA 40.78 41.57 44.54 39.40 NA NA 28 30.39 38.5637.48 36.32 35.10 35.76 35.01 35.68 29 528.80 449.28 403.09 381.85521.60 198.09 371.13 260.02 30 9.46 10.86 8.19 6.86 8.72 4.02 6.55 6.9931 3534.00 2342.20 3232.80 2522.40 3492.60 3012.20 3953.80 1768.25 321.57 0.00 1.22 1.68 1.76 0.80 1.27 1.79 33 6.00 6.00 1.50 1.75 4.50 1.005.00 3.50 34 218.94 205.59 187.77 242.99 169.32 257.81 238.23 208.44 355.69 5.99 5.67 5.51 5.26 4.91 6.00 6.04 36 19.10 29.78 24.08 15.14 13.0515.31 10.75 26.02 37 22.53 24.50 22.27 18.40 15.80 38.27 18.86 24.17 3822.33 19.33 22.93 24.87 25.00 46.00 24.33 18.00 39 92.90 3.26 66.4497.85 105.58 41.19 81.76 67.21 40 3.54 3.85 5.33 4.00 3.91 3.09 3.773.78 41 3.58 1.45 4.82 3.54 3.50 1.61 0.81 0.74 42 77.40 95.87 120.8072.47 60.40 138.20 70.53 92.17 43 79.80 29.21 96.73 88.40 87.89 77.9320.00 14.00 44 NA NA NA NA NA 2.88 0.39 0.86 45 13.66 NA 18.27 14.8014.49 17.03 9.99 7.13 46 74.93 57.59 87.49 74.52 68.16 77.53 56.83 69.9647 0.95 1.31 2.16 1.46 1.04 1.35 NA NA 48 0.51 0.51 0.63 0.52 0.54 0.380.39 1.16

TABLE 152 Measured parameters in bean varieties (lines 17-24) Ecotype/Line- Line- Line- Line- Line- Line- Treatment Line-17 18 19 Line-20 2122 23 24 1 85.44 NA 73.90 74.34 73.43 66.50 84.42 87.02 2 88.76 91.4891.63 81.98 91.83 72.86 83.06 92.96 3 68.87 82.92 59.82 55.76 76.9565.28 64.09 73.52 4 144.60 380.80 72.75 186.27 185.58 107.37 121.34205.43 5 23.50 26.63 15.58 33.63 35.09 31.03 18.65 32.50 6 8.30 11.988.02 10.31 13.50 9.34 6.97 10.69 7 0.39 0.93 0.24 0.34 0.59 0.38 0.360.51 8 NA NA NA 110.03 NA 49.94 49.06 NA 9 26.25 19.00 49.75 31.00 37.7522.25 23.25 24.25 10 40.09 35.22 42.84 46.31 52.08 22.62 32.83 26.57 1135.03 36.25 28.70 34.90 36.98 NA 51.24 16.45 12 0.83 0.90 0.81 1.00 1.061.07 1.18 0.71 13 12.64 10.70 12.64 12.32 11.11 11.99 12.79 13.98 148.47 7.92 7.78 8.04 7.69 7.61 7.52 8.93 15 211.60 529.13 192.00 206.36305.93 273.47 180.73 197.20 16 1.49 1.35 1.63 1.53 1.45 1.58 1.70 1.5717 4.40 8.33 5.87 4.83 4.27 6.13 4.13 3.80 18 8.87 5.73 9.20 6.87 7.608.87 9.00 7.53 19 4.20 7.40 5.50 4.63 3.89 6.00 6.00 5.00 20 6.51 6.706.74 5.91 5.56 6.77 7.02 8.15 21 4.89 NA 3.73 3.69 3.59 2.88 5.16 4.4922 3.82 5.59 2.25 2.40 4.79 3.34 3.63 3.43 23 32.26 39.72 30.44 38.6843.13 41.27 44.56 29.97 24 4.28 9.29 4.68 5.55 7.06 6.16 5.54 7.23 2510.47 25.33 11.23 12.67 18.33 15.33 11.67 13.30 26 16.39 16.43 19.4821.19 18.02 18.88 15.89 21.26 27 35.16 NA NA 41.68 42.06 43.01 42.3431.11 28 32.53 34.72 35.75 32.77 37.16 35.13 34.16 31.92 29 550.81595.35 431.52 568.44 526.18 533.60 482.22 456.91 30 9.63 10.35 7.9212.65 11.08 9.62 9.05 12.66 31 3804.20 1569.60 5946.60 3054.60 3368.604920.20 3978.60 2220.60 32 1.57 0.87 0.00 2.40 2.68 0.73 1.23 0.84 333.00 1.50 8.75 5.00 7.00 0.50 1.75 0.50 34 216.30 246.68 248.17 192.00200.55 237.69 220.62 223.74 35 5.39 5.98 5.29 5.24 6.13 5.54 5.54 5.7636 23.61 29.91 21.88 31.96 27.07 23.49 18.86 35.40 37 24.40 13.80 44.0725.67 23.42 33.93 30.00 25.53 38 23.67 13.80 30.27 31.67 26.56 27.3322.25 24.80 39 73.38 53.96 2.98 85.80 144.79 42.96 82.63 38.90 40 4.333.26 3.87 3.75 4.05 3.78 3.66 4.16 41 0.68 2.63 1.58 1.72 3.15 3.15 2.522.45 42 108.57 45.93 168.40 101.14 94.27 128.80 98.53 107.67 43 18.5034.73 50.13 71.08 79.58 84.60 58.55 75.20 44 NA NA NA 2.76 NA 2.30 1.53NA 45 8.33 9.80 12.29 11.46 17.94 13.71 NA 18.26 46 60.35 67.95 47.6676.06 79.67 70.77 70.87 108.68 47 1.22 1.37 1.52 NA 0.54 1.39 0.84 0.8748 0.41 0.65 0.45 0.65 0.85 0.58 0.35 0.73

TABLE 153 Measured parameters in bean varieties (lines 25-32) Ecotype/Line- Line- Line- Line- Line- Line- Treatment Line-25 Line-26 27 28 2930 31 32 1 78.37 NA NA 83.89 NA NA NA 83.40 2 62.46 80.32 86.63 82.5380.62 84.95 83.35 84.21 3 34.52 52.98 89.99 62.34 77.29 70.92 63.4261.26 4 154.53 158.50 120.75 96.79 207.74 307.17 116.14 94.55 5 29.3225.75 21.95 21.76 38.29 39.74 17.00 18.75 6 10.57 9.51 11.21 6.31 11.8710.37 11.99 10.58 7 0.45 0.47 0.54 0.21 0.58 0.68 0.48 0.36 8 82.58 NA76.18 NA 44.84 NA NA 61.66 9 43.50 19.75 28.25 32.00 29.25 21.75 32.7534.17 10 38.16 33.83 31.13 46.08 55.37 29.67 28.64 20.56 11 36.95 5.3051.21 37.34 45.13 NA 58.24 82.14 12 0.78 1.04 1.30 0.94 1.03 1.04 0.980.88 13 12.75 12.57 12.17 10.39 12.74 12.48 11.16 13.10 14 7.95 8.507.73 6.26 7.91 7.36 7.05 8.23 15 175.33 216.47 324.07 175.80 296.67394.11 242.20 200.60 16 1.61 1.49 1.58 1.67 1.62 1.69 1.59 1.59 17 4.444.53 7.17 7.00 5.78 7.22 6.19 5.13 18 5.22 7.93 6.94 8.27 6.25 7.89 6.538.20 19 4.33 4.40 6.92 7.60 5.38 9.00 6.40 8.40 20 4.86 6.67 7.40 6.215.81 6.62 6.42 8.40 21 3.58 NA NA 4.78 NA NA NA 4.67 22 1.27 2.60 6.303.50 4.11 4.15 3.07 2.66 23 29.44 41.58 53.17 34.74 41.54 44.37 37.4935.73 24 4.83 4.95 6.16 4.33 6.06 7.28 6.53 4.61 25 9.44 16.20 23.177.83 16.96 21.00 19.13 10.50 26 21.67 19.03 17.87 11.83 17.93 19.4417.01 11.16 27 39.99 NA NA 34.00 NA NA NA 37.81 28 35.57 34.99 34.5030.78 40.98 35.59 38.38 37.03 29 243.58 611.10 290.77 426.57 701.11487.72 501.09 102.62 30 7.97 10.63 5.42 7.37 11.01 12.46 8.24 1.94 311317.00 3861.60 2416.50 4403.00 3368.50 1595.00 4356.20 1164.40 32 2.321.06 1.47 1.40 0.00 1.99 0.90 0.61 33 3.50 0.75 2.00 6.25 6.75 0.25 2.250.83 34 199.91 210.95 250.40 236.94 211.71 257.52 203.46 211.37 35 6.696.01 6.05 5.09 5.14 5.72 5.65 6.28 36 26.12 21.54 13.01 18.17 25.1219.18 18.92 9.77 37 38.56 23.67 22.06 25.20 17.00 11.56 24.07 23.53 3830.67 18.60 23.17 25.33 19.33 17.11 24.93 32.40 39 109.63 71.71 91.0385.27 4.47 69.78 62.23 36.42 40 2.32 3.95 3.08 4.79 4.35 4.10 4.27 3.0241 3.07 1.78 0.35 3.65 2.88 3.44 4.93 2.48 42 85.44 90.13 65.11 118.0773.08 46.33 103.20 70.33 43 94.73 33.53 12.54 91.07 54.50 56.78 97.0781.40 44 6.16 NA 1.01 NA 3.36 NA NA 3.74 45 17.51 7.69 8.80 11.70 13.2015.19 12.91 18.53 46 105.57 57.22 66.76 61.77 75.61 82.68 69.11 86.77 470.97 1.56 1.65 0.93 1.28 NA NA 0.37 48 NA 0.44 0.69 0.39 0.66 NA 0.640.54

TABLE 154 Measured parameters in bean varieties (lines 33-40) Ecotype/Line- Line- Line- Line- Line- Treatment Line-33 Line-34 35 Line-36 37 3839 40 1 NA NA 88.31 79.59 NA 75.12 86.49 83.55 2 73.07 86.20 85.38 71.4187.69 68.05 78.62 83.74 3 38.21 80.07 69.51 40.26 77.04 26.24 52.9083.07 4 82.93 442.79 140.28 111.76 172.62 70.74 332.33 234.20 5 14.7830.35 17.92 18.54 27.13 15.10 42.93 33.72 6 7.35 8.81 9.00 7.44 10.395.21 11.57 14.47 7 0.20 0.88 0.34 0.30 0.53 0.21 0.52 0.77 8 23.67 NA54.00 89.21 60.88 NA NA NA 9 46.50 23.75 34.00 23.50 31.00 68.75 36.7519.50 10 46.23 50.20 32.68 23.70 61.33 22.64 25.53 29.43 11 44.70 48.7726.60 NA 35.90 71.49 18.99 7.42 12 0.79 0.94 0.98 0.96 1.03 0.71 1.021.59 13 11.79 13.38 11.47 11.63 13.44 12.88 12.46 11.64 14 7.10 8.568.12 7.33 8.47 8.68 8.12 8.13 15 174.00 442.20 197.27 146.89 210.3661.67 288.78 463.80 16 1.66 1.56 1.41 1.59 1.59 1.48 1.54 1.43 17 4.537.87 5.83 5.11 5.47 3.64 6.72 7.80 18 6.93 6.67 7.40 8.67 6.67 10.676.60 7.33 19 6.20 5.00 6.20 6.00 5.60 4.60 6.83 6.50 20 5.11 7.14 7.544.66 5.71 4.56 6.59 6.65 21 NA NA 5.55 4.20 NA 4.01 4.92 4.87 22 1.144.89 4.29 1.28 4.73 0.76 2.32 5.49 23 29.54 45.00 36.67 34.89 39.5826.25 40.51 60.87 24 3.46 9.08 4.25 4.98 6.69 3.50 5.44 6.36 25 8.7025.73 13.07 8.72 17.17 5.90 12.47 22.70 26 12.83 17.06 15.57 20.16 18.7319.53 23.90 23.34 27 NA NA 37.33 31.09 NA 34.70 32.23 39.56 28 34.2131.77 33.73 26.07 34.14 29.34 32.16 37.90 29 170.90 623.84 418.30 334.59551.91 330.59 604.79 695.47 30 3.70 10.27 8.21 9.76 10.68 10.16 16.1915.15 31 2036.80 1410.20 2980.60 2987.20 3196.80 4661.80 1823.80 3141.0032 0.00 0.00 1.36 1.66 0.00 1.03 1.70 0.90 33 9.50 5.50 2.00 0.00 9.003.25 1.50 1.50 34 255.60 271.09 234.43 228.00 266.51 251.56 239.50223.15 35 5.55 5.18 5.94 5.64 5.00 4.63 7.15 6.32 36 23.52 31.44 17.4724.60 25.46 28.08 37.91 28.98 37 63.57 13.93 19.53 24.53 18.47 43.9327.00 20.13 38 26.87 13.73 23.00 22.33 11.92 43.40 32.00 22.27 39 1.793.03 83.19 52.44 3.82 40.39 68.98 53.52 40 1.82 3.39 3.76 5.30 4.92 5.122.89 4.23 41 1.12 1.79 2.47 1.83 1.28 1.42 1.91 3.05 42 111.93 47.8773.20 126.73 93.20 224.00 76.33 84.73 43 31.71 22.87 57.07 45.43 16.4762.29 59.33 58.80 44 0.30 NA 1.67 1.54 1.01 NA NA NA 45 10.76 14.3111.87 17.40 NA 14.32 27.62 14.82 46 52.76 71.50 80.20 116.85 59.77 71.51156.73 80.57 47 1.39 NA 1.58 1.43 NA 1.34 1.36 2.03 48 0.42 0.60 0.540.36 0.68 0.25 0.79 0.89

TABLE 155 Measured parameters in bean varieties (“fine” and “extrafine”) (lines 1-8) Ecotype/ Treatment Line-1 Line-2 Line-3 Line-4 Line-5Line-6 Line-7 Line-8 1 88.66 91.02 80.76 90.29 84.27 NA 73.90 66.50 289.59 78.87 72.28 90.49 73.78 76.45 91.63 72.86 3 70.53 58.56 38.9883.64 46.91 51.88 59.82 65.28 4 94.43 117.59 69.63 123.75 66.31 93.6872.75 107.37 5 16.19 18.66 19.29 27.82 14.44 18.02 15.58 31.03 6 7.338.28 6.37 11.85 5.42 7.40 8.02 9.34 7 0.30 0.33 0.24 0.44 0.21 0.35 0.240.38 8 NA 67.40 38.22 76.45 49.40 43.69 NA 49.94 9 24.25 35.25 65.0026.50 38.75 35.50 49.75 22.25 10 19.39 40.69 36.57 19.08 17.38 41.3642.84 22.62 11 NA 48.72 38.91 67.38 41.28 55.89 28.70 NA 12 0.97 0.850.91 0.85 0.72 1.06 0.81 1.07 13 13.34 11.64 11.14 13.15 11.99 12.3512.64 11.99 14 8.16 8.83 7.03 8.42 7.85 8.13 7.78 7.61 15 211.67 307.13133.13 308.07 157.53 155.00 192.00 273.47 16 1.64 1.32 1.58 1.56 1.531.52 1.63 1.58 17 4.73 6.07 4.73 6.17 5.00 5.42 5.87 6.13 18 7.93 6.207.93 7.00 9.67 7.53 9.20 8.87 19 4.90 4.90 5.80 6.60 5.10 5.70 5.50 6.0020 8.44 7.85 5.78 7.61 6.29 6.60 6.74 6.77 21 6.15 5.84 4.38 4.01 4.95NA 3.73 2.88 22 3.27 3.06 1.33 5.01 1.58 1.74 2.25 3.34 23 36.84 34.8331.52 37.71 28.88 39.83 30.44 41.27 24 4.39 4.80 3.68 5.75 3.93 4.504.68 6.16 25 11.43 11.17 7.60 16.57 8.40 9.67 11.23 15.33 26 11.67 15.2015.96 23.07 17.06 15.12 19.48 18.88 27 40.19 36.22 37.68 NA 39.40 NA NA43.01 28 36.00 39.44 31.41 40.15 35.76 35.01 35.75 35.13 29 342.44457.16 196.69 430.61 198.09 371.13 431.52 533.60 30 6.31 8.29 4.53 9.204.02 6.55 7.92 9.62 31 3635.20 3879.60 2875.20 3485.80 3012.20 3953.805946.60 4920.20 32 0.62 2.06 1.15 0.60 0.80 1.27 0.00 0.73 33 0.50 6.009.50 1.50 1.00 5.00 8.75 0.50 34 226.25 222.25 213.00 207.31 257.81238.23 248.17 237.69 35 5.79 5.84 5.40 5.83 4.91 6.00 5.29 5.54 36 12.7620.71 13.89 30.42 15.31 10.75 21.88 23.49 37 27.13 24.73 46.07 38.2738.27 18.86 44.07 33.93 38 33.07 33.93 31.58 20.94 46.00 24.33 30.2727.33 39 32.96 105.04 61.14 33.15 41.19 81.76 2.98 42.96 40 3.32 4.682.81 3.93 3.09 3.77 3.87 3.78 41 2.64 2.35 1.02 0.63 1.61 0.81 1.58 3.1542 90.47 111.33 128.60 151.80 138.20 70.53 168.40 128.80 43 87.60 79.0029.38 9.17 77.93 20.00 50.13 84.60 44 NA 3.45 0.50 0.17 2.88 0.39 NA2.30 45 16.30 13.53 18.80 12.64 17.03 9.99 12.29 13.71 46 91.61 65.6561.83 71.07 77.53 56.83 47.66 70.77 47 0.92 2.03 1.67 0.84 1.35 NA 1.521.39 48 0.44 0.46 0.35 1.18 0.38 0.39 0.45 0.58

TABLE 156 Measured parameters in bean varieties (“fine” and “extrafine”) (lines 9-16) Ecotype/ Line- Line- Line- Line- Line- TreatmentLine-9 Line-10 Line-11 12 13 14 15 16 1 84.42 NA 83.89 NA 83.40 NA 79.5975.12 2 83.06 86.63 82.53 83.35 84.21 73.07 71.41 68.05 3 64.09 89.9962.34 63.42 61.26 38.21 40.26 26.24 4 121.34 120.75 96.79 116.14 94.5582.93 111.76 70.74 5 18.65 21.95 21.76 17.00 18.75 14.78 18.54 15.10 66.97 11.21 6.31 11.99 10.58 7.35 7.44 5.21 7 0.36 0.54 0.21 0.48 0.360.20 0.30 0.21 8 49.06 76.18 NA NA 61.66 23.67 89.21 NA 9 23.25 28.2532.00 32.75 34.17 46.50 23.50 68.75 10 32.83 31.13 46.08 28.64 20.5646.23 23.70 22.64 11 51.24 51.21 37.34 58.24 82.14 44.70 NA 71.49 121.18 1.30 0.94 0.98 0.88 0.79 0.96 0.71 13 12.79 12.17 10.39 11.16 13.1011.79 11.63 12.88 14 7.52 7.73 6.26 7.05 8.23 7.10 7.33 8.68 15 180.73324.07 175.80 242.20 200.60 174.00 146.89 61.67 16 1.70 1.58 1.67 1.591.59 1.66 1.59 1.48 17 4.13 7.17 7.00 6.19 5.13 4.53 5.11 3.64 18 9.006.94 8.27 6.53 8.20 6.93 8.67 10.67 19 6.00 6.92 7.60 6.40 8.40 6.206.00 4.60 20 7.02 7.40 6.21 6.42 8.40 5.11 4.66 4.56 21 5.16 NA 4.78 NA4.67 NA 4.20 4.01 22 3.63 6.30 3.50 3.07 2.66 1.14 1.28 0.76 23 44.5653.17 34.74 37.49 35.73 29.54 34.89 26.25 24 5.54 6.16 4.33 6.53 4.613.46 4.98 3.50 25 11.67 23.17 7.83 19.13 10.50 8.70 8.72 5.90 26 15.8917.87 11.83 17.01 11.16 12.83 20.16 19.53 27 42.34 NA 34.00 NA 37.81 NA31.09 34.70 28 34.16 34.50 30.78 38.38 37.03 34.21 26.07 29.34 29 482.22290.77 426.57 501.09 102.62 170.90 334.59 330.59 30 9.05 5.42 7.37 8.241.94 3.70 9.76 10.16 31 3978.60 2416.50 4403.00 4356.20 1164.40 2036.802987.20 4661.80 32 1.23 1.47 1.40 0.90 0.61 0.00 1.66 1.03 33 1.75 2.006.25 2.25 0.83 9.50 0.00 3.25 34 220.62 250.40 236.94 203.46 211.37255.60 228.00 251.56 35 5.54 6.05 5.09 5.65 6.28 5.55 5.64 4.63 36 18.8613.01 18.17 18.92 9.77 23.52 24.60 28.08 37 30.00 22.06 25.20 24.0723.53 63.57 24.53 43.93 38 22.25 23.17 25.33 24.93 32.40 26.87 22.3343.40 39 82.63 91.03 85.27 62.23 36.42 1.79 52.44 40.39 40 3.66 3.084.79 4.27 3.02 1.82 5.30 5.12 41 2.52 0.35 3.65 4.93 2.48 1.12 1.83 1.4242 98.53 65.11 118.07 103.20 70.33 111.93 126.73 224.00 43 58.55 12.5491.07 97.07 81.40 31.71 45.43 62.29 44 1.53 1.01 NA NA 3.74 0.30 1.54 NA45 NA 8.80 11.70 12.91 18.53 10.76 17.40 14.32 46 70.87 66.76 61.7769.11 86.77 52.76 116.85 71.51 47 0.84 1.65 0.93 NA 0.37 1.39 1.43 1.3448 0.35 0.69 0.39 0.64 0.54 0.42 0.36 0.25

TABLE 157 Correlation between the expression level of selected genes ofsome embodiments of the invention in various tissues and the phenotypicperformance under normal conditions across 40 bean varieties Gene Exp.Corr. Gene Exp. Corr. Name R P value set Set ID Name R P value set SetID LGP84  0.72 1.22E−02 4 27 LGP84  0.76 1.06E−04 4 46 LGP84  0.794.04E−03 9 27 LGP85  0.72 3.25E−04 9 40 LYD701 0.73 6.02E−04 2 9 LYD7020.81 1.50E−06 5 43 LYD702 0.74 1.79E−03 5 44 LYD702 0.73 2.86E−03 3 27LYD702 0.75 6.21E−07 6 38 LYD703 0.87 1.17E−03 2 27 LYD705 0.85 1.18E−075 46 LYD705 0.77 7.09E−04 5 44 LYD706 0.73 2.69E−04 9 9 LYD706 0.82.55E−06 5 43 LYD706 0.79 4.18E−04 5 44 LYD713 0.72 1.70E−03 1 44 LYD7130.83 1.92E−05 2 25 LYD713 0.73 1.55E−02 2 27 LYD713 0.75 3.27E−04 2 23LYD717 0.73 2.62E−04 9 4 LYD717 0.71 2.24E−04 7 29 LYD718 0.78 3.29E−041 44 LYD718 0.77 6.00E−05 9 33 LYD719 0.76 5.46E−05 3 46 LYD720 0.721.28E−02 4 27 LYD721 0.76 1.18E−04 9 33 LYD722 0.76 2.37E−04 2 43 LYD7220.72 6.72E−04 2 41 LYD722 0.77 8.76E−04 2 44 LYD722 0.76 1.04E−04 7 48LYD723 0.76 1.06E−03 2 44 LYD723 0.71 9.72E−05 5 43 LYD723 0.75 1.39E−035 44 LYD723 0.71 1.01E−03 7 45 LYD725 0.71 4.61E−03 2 45 LYD725 0.731.31E−04 7 38 LYD726 0.71 3.33E−03 7 8 LYD727 0.75 2.95E−03 2 1 LYD7290.72 3.83E−04 4 28 LYD729 0.75 3.10E−03 2 21 LYD731 0.82 3.47E−05 2 4LYD731 0.76 2.75E−04 2 7 LYD731 0.7 2.61E−04 7 22 LYD731 0.75 5.02E−03 68 LYD733 0.72 2.27E−04 6 1 LYD738 0.7 1.15E−03 2 14 LYD738 0.8 7.29E−052 28 LYD739 0.72 1.74E−04 7 5 LYD739 0.71 1.04E−03 2 9 LYD739 0.721.67E−04 7 46 LYD739 0.75 1.21E−03 7 8 LYD742 0.73 2.42E−04 9 20 LYD7420.71 9.42E−04 2 19 LYD745 0.75 1.26E−04 9 42 LYD742 0.7 5.50E−04 9 23LYD747 0.77 8.34E−05 9 33 LYD745 0.75 6.72E−05 7 17 LYD749 0.7 2.41E−022 27 LYD748 0.75 2.99E−04 2 2 LYD750 0.73 2.36E−04 4 42 LYD749 0.713.08E−04 3 48 LYD752 0.72 2.60E−03 5 1 LYD752 0.77 7.05E−04 5 21 LYD7530.76 2.79E−04 2 46 LYD753 0.72 6.87E−04 2 43 LYD753 0.74 3.04E−05 5 43LYD753 0.8 3.10E−04 2 44 LYD754 0.75 1.52E−04 4 37 LYD753 0.81 2.86E−045 44 LYD754 0.73 5.42E−05 5 42 LYD754 0.83 6.15E−06 9 37 LYD755 0.751.35E−04 9 10 LYD754 0.76 1.71E−05 5 37 LYD756 0.7 5.38E−04 9 4 LYD7550.76 4.20E−03 5 27 LYD761 0.72 2.50E−03 7 8 LYD757 0.75 7.31E−03 3 8LYD765 0.73 2.92E−04 4 7 LYD765 0.71 1.04E−06 1 37 LYD765 0.72 3.84E−049 4 LYD765 0.7 1.14E−03 2 38 LYD765 0.79 1.87E−05 3 3 LYD765 0.731.53E−04 3 22 LYD768 0.71 9.74E−04 2 19 LYD767 0.76 6.24E−04 1 44 LYD7680.84 2.20E−07 5 4 LYD768 0.77 4.81E−04 2 11 LYD769 0.78 2.06E−05 7 46LYD769 0.71 9.51E−04 2 3 LYD771 0.73 5.44E−04 2 43 LYD773 0.71 9.72E−042 46 LYD774 0.75 2.52E−05 5 46 LYD776 0.78 5.36E−05 4 13 LYD776 0.735.17E−04 2 46 LYD777 0.7 2.30E−02 2 27 LYD777 0.7 5.59E−04 9 9 LYD7800.71 3.26E−03 5 44 LYD780 0.71 3.35E−04 3 46 LYD782 0.74 4.11E−03 2 21LYD782 0.71 6.28E−03 2 1 LYD783 0.76 1.03E−04 9 4 LYD783 0.71 1.44E−06 87 LYD785 0.8 2.42E−06 5 46 LYD788 0.71 6.72E−03 2 21 LYD788 0.8 2.14E−043 21 LYD791 0.73 2.87E−04 9 9 LYD791 0.8 2.36E−05 9 33 LYD794 0.733.42E−04 4 48 LYD795 0.84 1.33E−03 4 27 LYD796 0.76 6.14E−05 3 37 LYD7970.73 1.02E−02 3 44 LYD798 0.71 4.06E−04 9 32 LYD798 0.71 1.38E−03 9 44LYD798 0.83 1.32E−04 7 8 LYD803 0.71 4.87E−04 4 7 LYD803 0.72 2.29E−03 78 LYD809 0.75 2.44E−05 5 46 LYD810 0.76 2.92E−04 2 46 LYD810 0.712.12E−04 7 4 LYD810 0.7 2.84E−04 7 7 LYD811 0.72 8.51E−04 2 38 LYD8110.84 2.52E−05 2 48 LYD812 0.77 5.47E−04 1 8 LYD815 0.7 1.30E−04 5 24LYD815 0.71 1.09E−04 5 7 LYD816 0.75 1.33E−03 2 8 LYD817 0.78 1.26E−04 411 LYD817 0.72 8.38E−04 2 38 LYD818 0.71 1.08E−06 1 4 LYD821 0.726.98E−04 2 46 LYD822 0.77 9.28E−06 5 24 LYD822 0.74 4.11E−05 5 4 LYD8220.74 3.64E−05 5 25 LYD822 0.78 6.34E−06 5 7 LYD822 0.71 1.03E−04 5 15LYD823 0.73 2.86E−04 9 7 LYD826 0.73 1.01E−02 3 44 LYD827 0.72 6.55E−055 46 LYD829 0.77 5.02E−05 3 4 LYD829 0.73 1.98E−04 3 25 LYD830 0.726.86E−05 5 43 LYD830 0.77 7.63E−04 5 44 LYD927 0.7 1.85E−06 8 20 LYD9300.79 2.88E−05 9 10 Provided are the correlations (R) between theexpression levels yield improving genes and their homologs in varioustissues [Expression (Exp) sets] and the phenotypic performance [yield,biomass, and plant architecture (Correlation vector (Cor))] under normalconditions across bean varieties. P = p value.

TABLE 158 Correlation between the expression level of selected genes ofsome embodiments of the invention in various tissues and the phenotypicperformance under normal conditions across 16 bean varieties (“fine” and“extra fine”) Gene Exp. Corr. Gene Exp. Corr. Name R P value set Set IDName R P value set Set ID LGP71 0.85 9.05E−04 2 46 LGP71 0.71 1.46E−02 338 LGP71 0.74 9.69E−03 3 45 LGP71 0.71 4.75E−02 3 11 LGP71 0.74 6.41E−036 18 LGP84 0.78 7.37E−03 1 27 LGP84 0.71 2.09E−03 1 6 LGP84 0.861.28E−02 4 27 LGP84 0.85 3.94E−04 4 46 LGP84 0.73 1.65E−02 4 11 LGP840.77 1.58E−02 2 21 LGP84 0.73 6.95E−03 9 32 LGP84 0.80 2.90E−02 9 27LGP84 0.71 3.36E−02 9 1 LGP84 0.73 1.00E−02 9 8 LGP84 0.73 6.65E−03 9 46LGP84 0.81 5.25E−02 5 27 LGP84 0.71 2.20E−03 8 24 LGP84 0.73 1.42E−03 87 LGP84 0.71 2.23E−02 7 18 LGP84 0.74 1.34E−02 7 13 LGP84 0.84 1.80E−023 27 LGP84 0.72 4.33E−02 3 11 LGP84 0.70 1.10E−02 6 42 LGP84 0.773.65E−03 6 26 LGP84 0.77 3.22E−03 6 36 LGP84 0.81 1.50E−03 6 30 LGP840.87 2.37E−02 6 27 LGP85 0.87 2.62E−04 4 48 LGP85 0.82 2.14E−03 2 40LGP85 0.79 3.90E−03 2 46 LGP85 0.75 4.62E−03 9 40 LGP85 0.74 9.57E−03 55 LGP85 0.79 2.61E−04 8 48 LGP85 0.77 1.53E−02 7 8 LGP85 0.79 6.87E−03 740 LGP85 0.76 8.01E−02 6 27 LGP85 0.73 6.66E−03 6 5 LYD701 0.80 1.86E−041 9 LYD701 0.73 7.46E−03 4 37 LYD701 0.73 1.04E−02 2 24 LYD701 0.803.36E−03 2 9 LYD701 0.85 9.18E−04 2 25 LYD701 0.76 6.15E−03 2 33 LYD7010.71 1.52E−02 2 7 LYD701 0.80 3.45E−03 2 22 LYD701 0.74 9.78E−03 2 3LYD701 0.82 1.10E−03 9 32 LYD701 0.86 2.67E−03 9 21 LYD701 0.83 7.71E−049 39 LYD701 0.78 4.64E−03 3 33 LYD701 0.84 1.29E−03 3 37 LYD701 0.731.09E−02 3 48 LYD701 0.74 5.47E−03 6 9 LYD701 0.72 8.38E−03 6 33 LYD7020.90 1.83E−04 5 43 LYD702 0.80 3.17E−03 5 41 LYD702 0.81 5.22E−02 5 27LYD702 0.83 5.84E−03 5 44 LYD702 0.72 1.23E−02 3 41 LYD702 0.82 1.02E−036 18 LYD702 0.81 1.38E−03 6 38 LYD702 0.81 2.60E−02 6 44 LYD703 0.832.06E−02 4 27 LYD703 0.97 3.23E−04 2 27 LYD703 0.77 3.52E−03 9 39 LYD7030.93 7.80E−03 5 27 LYD703 0.75 8.42E−04 8 4 LYD703 0.72 1.56E−03 8 5LYD703 0.71 1.90E−03 8 48 LYD703 0.70 2.41E−03 8 3 LYD703 0.90 3.75E−047 2 LYD703 0.79 6.07E−03 7 20 LYD703 0.82 3.76E−03 7 28 LYD703 0.779.62E−03 7 14 LYD703 0.80 3.01E−02 7 27 LYD703 0.74 1.52E−02 7 48 LYD7030.76 1.02E−02 7 22 LYD703 0.86 1.61E−03 7 3 LYD703 0.90 3.26E−04 7 13LYD703 0.76 6.75E−03 3 28 LYD703 0.71 1.40E−02 3 7 LYD703 0.83 1.96E−023 27 LYD703 0.85 9.45E−04 3 15 LYD703 0.71 1.36E−02 3 6 LYD703 0.778.68E−03 6 11 LYD704 0.88 1.55E−03 9 21 LYD704 0.79 1.10E−02 9 1 LYD7040.78 4.25E−03 5 41 LYD704 0.71 2.17E−02 7 2 LYD704 0.78 6.63E−02 6 27LYD705 0.70 2.48E−03 1 41 LYD705 0.75 4.72E−03 4 34 LYD705 0.74 9.38E−035 43 LYD705 0.72 1.29E−02 5 41 LYD705 0.73 2.48E−02 5 44 LYD705 0.761.15E−02 7 2 LYD705 0.73 2.61E−02 7 8 LYD705 0.80 2.90E−03 3 45 LYD7050.75 1.30E−02 6 11 LYD706 0.71 2.18E−03 1 31 LYD706 0.78 2.50E−03 9 9LYD706 0.78 2.87E−03 9 33 LYD706 0.86 6.34E−04 5 43 LYD706 0.90 1.65E−045 41 LYD706 0.73 1.63E−02 7 2 LYD706 0.84 1.22E−03 3 46 LYD706 0.814.78E−03 6 11 LYD707 0.75 5.36E−03 4 43 LYD707 0.80 1.69E−03 4 38 LYD7070.72 1.90E−02 2 44 LYD707 0.74 8.52E−03 5 43 LYD707 0.71 3.22E−02 5 44LYD707 0.91 6.31E−04 7 8 LYD707 0.76 1.12E−02 7 40 LYD707 0.70 2.41E−027 46 LYD707 0.79 3.93E−03 3 46 LYD707 0.73 7.24E−03 6 30 LYD708 0.719.04E−03 4 10 LYD708 0.70 1.57E−02 2 2 LYD708 0.78 4.84E−03 2 20 LYD7080.74 9.47E−03 2 28 LYD708 0.75 5.00E−02 2 27 LYD708 0.75 8.11E−03 2 15LYD708 0.79 3.91E−03 2 22 LYD708 0.77 5.64E−03 2 3 LYD708 0.79 1.21E−029 21 LYD708 0.77 3.66E−03 9 39 LYD708 0.82 1.83E−03 5 33 LYD708 0.702.28E−02 7 18 LYD708 0.71 2.02E−02 7 34 LYD708 0.82 1.87E−03 3 48 LYD7100.81 2.77E−03 2 43 LYD710 0.70 1.65E−02 2 41 LYD710 0.81 4.73E−03 2 44LYD710 0.85 9.84E−04 5 43 LYD710 0.85 3.90E−03 5 44 LYD710 0.70 2.49E−038 9 LYD710 0.71 2.06E−02 7 28 LYD710 0.83 2.83E−03 7 14 LYD710 0.712.15E−02 7 15 LYD710 0.77 9.83E−03 7 22 LYD710 0.80 9.51E−03 7 1 LYD7100.71 2.20E−02 7 3 LYD710 0.84 1.35E−03 3 43 LYD710 0.82 1.84E−03 3 41LYD710 0.80 1.68E−02 3 44 LYD710 0.73 6.72E−03 6 32 LYD710 0.77 3.40E−036 20 LYD710 0.72 6.88E−02 6 8 LYD711 0.76 6.95E−04 1 42 LYD711 0.779.33E−03 7 48 LYD711 0.84 1.72E−02 3 27 LYD711 0.75 4.99E−03 6 42 LYD7110.83 9.15E−04 6 37 LYD713 0.73 7.29E−03 4 37 LYD713 0.75 8.03E−03 2 2LYD713 0.75 7.56E−03 2 24 LYD713 0.81 2.28E−03 2 20 LYD713 0.83 1.56E−032 28 LYD713 0.91 1.26E−04 2 25 LYD713 0.86 7.36E−04 2 7 LYD713 0.711.41E−02 2 12 LYD713 0.79 3.27E−02 2 27 LYD713 0.79 4.05E−03 2 17 LYD7130.81 2.68E−03 2 22 LYD713 0.79 3.56E−03 2 3 LYD713 0.83 1.39E−03 2 23LYD713 0.74 9.11E−03 2 6 LYD713 0.80 8.93E−03 2 11 LYD713 0.88 3.74E−042 13 LYD713 0.78 2.99E−03 9 9 LYD713 0.81 1.35E−03 9 33 LYD713 0.752.01E−02 9 1 LYD713 0.72 1.25E−02 5 17 LYD713 0.81 1.44E−02 5 1 LYD7130.74 1.12E−03 8 5 LYD713 0.80 3.37E−03 3 26 LYD713 0.75 8.38E−03 3 35LYD713 0.73 1.15E−02 3 25 LYD713 0.70 1.63E−02 3 7 LYD713 0.80 3.10E−033 48 LYD713 0.76 1.79E−02 3 1 LYD713 0.89 3.34E−03 3 11 LYD713 0.821.11E−03 6 19 LYD714 0.79 2.18E−03 4 20 LYD714 0.84 6.82E−04 4 28 LYD7140.88 1.91E−04 4 14 LYD714 0.73 7.54E−03 4 15 LYD714 0.77 3.38E−03 4 48LYD714 0.70 1.07E−02 4 6 LYD714 0.74 2.18E−02 2 21 LYD714 0.73 1.11E−022 14 LYD714 0.73 1.62E−02 5 45 LYD714 0.71 2.14E−02 7 15 LYD714 0.823.75E−03 7 48 LYD714 0.80 3.26E−03 3 43 LYD714 0.72 2.92E−02 3 21 LYD7140.77 6.08E−03 3 41 LYD714 0.88 3.51E−03 3 44 LYD714 0.88 4.25E−03 6 21LYD715 0.74 2.13E−02 2 11 LYD715 0.82 9.57E−04 9 32 LYD715 0.78 3.01E−039 39 LYD715 0.80 5.57E−03 7 19 LYD715 0.74 1.44E−02 7 20 LYD715 0.772.46E−02 7 11 LYD715 0.72 1.94E−02 7 13 LYD715 0.71 1.48E−02 3 16 LYD7170.72 8.69E−03 4 18 LYD717 0.80 3.38E−03 4 45 LYD717 0.84 1.11E−03 2 29LYD717 0.78 2.88E−03 9 4 LYD717 0.77 3.20E−03 9 39 LYD717 0.76 6.27E−035 40 LYD717 0.70 2.41E−02 7 15 LYD717 0.81 1.38E−03 6 4 LYD718 0.737.56E−03 4 43 LYD718 0.72 8.68E−03 4 41 LYD718 0.79 2.32E−03 4 46 LYD7180.76 1.15E−02 2 44 LYD718 0.70 1.09E−02 9 9 LYD718 0.84 6.89E−04 9 33LYD718 0.75 4.84E−03 9 10 LYD718 0.75 2.07E−02 9 1 LYD718 0.85 1.03E−035 43 LYD718 0.87 5.42E−04 5 41 LYD718 0.80 9.78E−03 5 44 LYD718 0.796.28E−03 7 2 LYD718 0.72 1.85E−02 7 20 LYD718 0.73 6.32E−02 7 27 LYD7180.71 2.04E−02 7 22 LYD718 0.76 9.98E−03 7 3 LYD718 0.84 2.27E−03 7 13LYD718 0.78 4.80E−03 3 4 LYD718 0.75 3.25E−02 3 44 LYD719 0.72 1.20E−024 45 LYD719 0.80 1.60E−03 4 46 LYD719 0.71 1.35E−02 4 44 LYD719 0.958.30E−05 9 21 LYD719 0.78 1.24E−02 9 1 LYD719 0.77 5.51E−03 5 42 LYD7190.81 2.78E−03 5 43 LYD719 0.89 2.02E−04 5 41 LYD719 0.71 5.08E−02 3 8LYD719 0.89 2.47E−04 3 46 LYD719 0.76 2.92E−02 3 11 LYD720 0.79 3.58E−024 27 LYD720 0.74 9.08E−03 2 5 LYD720 0.93 3.38E−04 2 11 LYD720 0.701.05E−02 9 32 LYD720 0.78 2.76E−03 9 39 LYD720 0.84 1.12E−03 5 43 LYD7200.88 3.63E−04 5 41 LYD720 0.76 1.86E−02 5 44 LYD720 0.84 2.22E−03 7 28LYD720 0.79 7.02E−03 7 14 LYD720 0.71 2.17E−02 7 48 LYD720 0.71 1.43E−023 28 LYD720 0.71 1.45E−02 3 15 LYD720 0.75 7.96E−03 3 48 LYD720 0.764.02E−03 6 32 LYD720 0.74 6.23E−03 6 39 LYD721 0.71 1.48E−02 2 43 LYD7210.72 2.00E−02 2 44 LYD721 0.82 1.16E−03 9 33 LYD721 0.70 1.06E−02 9 10LYD721 0.72 7.70E−03 9 37 LYD721 0.77 6.00E−03 5 43 LYD721 0.74 8.60E−035 41 LYD721 0.82 6.21E−03 5 44 LYD721 0.90 9.24E−04 7 21 LYD721 0.713.34E−02 7 1 LYD721 0.81 2.53E−03 3 45 LYD721 0.71 4.98E−02 6 21 LYD7210.70 1.10E−02 6 15 LYD721 0.80 3.05E−02 6 8 LYD721 0.70 1.12E−02 6 6LYD722 0.77 3.34E−03 4 34 LYD722 0.70 1.61E−02 2 43 LYD722 0.76 7.08E−032 41 LYD722 0.73 2.45E−02 9 21 LYD722 0.75 5.04E−03 9 14 LYD722 0.811.29E−03 9 39 LYD722 0.79 1.15E−02 9 1 LYD722 0.75 7.66E−03 5 38 LYD7220.70 2.36E−02 7 26 LYD722 0.79 5.99E−03 7 25 LYD722 0.73 1.65E−02 7 15LYD722 0.95 3.07E−05 7 48 LYD722 0.71 2.24E−02 7 17 LYD722 0.79 6.65E−037 22 LYD722 0.82 3.85E−03 7 3 LYD722 0.72 1.81E−02 7 6 LYD722 0.711.46E−02 3 28 LYD722 0.87 4.31E−04 3 48 LYD722 0.72 4.23E−02 3 11 LYD7230.73 6.93E−03 4 40 LYD723 0.84 1.25E−03 2 41 LYD723 0.85 2.04E−03 2 44LYD723 0.87 4.79E−04 5 43 LYD723 0.87 5.42E−04 5 41 LYD723 0.74 9.06E−035 38 LYD723 0.90 1.04E−03 5 44 LYD723 0.79 1.08E−02 7 1 LYD723 0.892.04E−04 3 43 LYD723 0.86 7.41E−04 3 41 LYD723 0.88 4.36E−03 3 44 LYD7250.75 5.27E−03 4 46 LYD725 0.72 1.86E−02 2 45 LYD725 0.75 7.43E−03 5 34LYD725 0.76 6.63E−03 3 9 LYD725 0.73 1.01E−02 3 43 LYD725 0.73 1.13E−023 41 LYD725 0.82 4.75E−02 6 27 LYD726 0.78 2.55E−03 4 37 LYD726 0.731.13E−02 2 24 LYD726 0.91 1.16E−04 2 25 LYD726 0.75 7.87E−03 2 7 LYD7260.72 1.31E−02 2 48 LYD726 0.71 1.37E−02 2 17 LYD726 0.87 5.37E−04 2 22LYD726 0.88 3.34E−04 2 3 LYD726 0.71 1.36E−02 2 6 LYD726 0.76 7.75E−02 527 LYD726 0.71 3.20E−02 7 1 LYD726 0.71 3.24E−02 7 8 LYD726 0.792.10E−03 6 30 LYD727 0.73 6.50E−03 4 28 LYD727 0.85 4.03E−03 9 21 LYD7270.73 6.50E−03 9 39 LYD727 0.74 5.45E−03 9 38 LYD727 0.83 6.01E−03 9 1LYD727 0.77 5.92E−03 5 20 LYD727 0.70 5.20E−02 5 1 LYD727 0.84 4.54E−035 8 LYD727 0.85 4.11E−03 3 21 LYD727 0.74 9.58E−03 3 46 LYD729 0.863.37E−04 4 28 LYD729 0.86 2.92E−04 4 14 LYD729 0.81 8.67E−03 2 21 LYD7290.79 4.06E−03 2 33 LYD729 0.76 3.94E−03 9 32 LYD729 0.85 3.73E−03 9 1LYD729 0.73 1.03E−02 9 8 LYD729 0.72 1.29E−02 5 43 LYD729 0.85 3.92E−035 44 LYD729 0.83 2.75E−03 7 20 LYD729 0.75 1.16E−02 7 14 LYD729 0.721.79E−02 7 7 LYD729 0.72 1.92E−02 7 22 LYD729 0.79 1.08E−02 7 8 LYD7290.76 2.91E−02 7 11 LYD729 0.73 6.36E−02 3 27 LYD729 0.75 7.86E−03 3 31LYD729 0.81 1.44E−03 6 35 LYD729 0.78 2.81E−03 6 12 LYD729 0.78 2.91E−036 23 LYD730 0.70 2.52E−03 1 41 LYD730 0.70 7.86E−02 4 27 LYD730 0.719.65E−03 4 37 LYD730 0.85 8.08E−04 2 20 LYD730 0.75 7.64E−03 2 28 LYD7300.79 3.58E−03 2 14 LYD730 0.70 1.61E−02 2 13 LYD730 0.78 2.64E−03 9 32LYD730 0.76 1.72E−02 9 21 LYD730 0.83 8.95E−04 9 39 LYD730 0.89 1.49E−039 1 LYD730 0.72 1.26E−02 5 43 LYD730 0.87 5.69E−04 5 41 LYD730 0.802.96E−02 7 27 LYD730 0.75 5.28E−03 6 26 LYD730 0.72 8.70E−03 6 38 LYD7310.78 4.83E−03 4 8 LYD731 0.89 6.27E−04 7 48 LYD731 0.78 7.15E−03 7 22LYD731 0.71 3.23E−02 7 1 LYD731 0.76 1.09E−02 7 3 LYD731 0.72 1.18E−02 324 LYD731 0.80 3.28E−03 3 4 LYD731 0.84 9.80E−03 3 8 LYD731 0.775.75E−03 3 46 LYD731 0.74 5.93E−03 6 12 LYD731 0.80 1.89E−03 6 22 LYD7310.74 3.70E−02 6 1 LYD731 0.76 4.51E−03 6 3 LYD731 0.82 1.22E−03 6 23LYD731 0.74 5.73E−02 6 8 LYD733 0.81 4.41E−04 1 47 LYD733 0.86 2.83E−039 21 LYD733 0.76 3.92E−03 9 39 LYD733 0.76 4.37E−03 9 31 LYD733 0.761.85E−02 9 1 LYD733 0.71 1.45E−02 5 43 LYD733 0.75 7.84E−03 5 41 LYD7330.78 7.90E−03 7 28 LYD733 0.71 2.27E−02 7 38 LYD733 0.72 1.27E−02 3 2LYD733 0.79 1.86E−02 6 21 LYD733 0.74 3.77E−02 6 1 LYD735 0.72 1.25E−025 5 LYD735 0.74 5.75E−02 4 27 LYD735 0.88 9.44E−03 7 27 LYD735 0.812.80E−02 9 27 LYD735 0.74 8.96E−03 3 24 LYD735 0.76 1.15E−02 7 25 LYD7350.71 1.52E−02 3 48 LYD735 0.72 1.86E−02 7 5 LYD735 0.70 1.05E−02 6 39LYD735 0.84 1.12E−03 3 5 LYD736 0.75 8.06E−03 5 42 LYD735 0.70 1.61E−023 6 LYD736 0.79 3.80E−03 5 48 LYD735 0.70 1.08E−02 6 17 LYD736 0.874.81E−03 7 11 LYD736 0.76 6.61E−03 5 26 LYD736 0.73 1.02E−02 3 41 LYD7360.77 1.50E−02 7 8 LYD737 0.77 5.12E−03 1 8 LYD736 0.74 8.87E−03 3 43LYD737 0.72 2.83E−02 2 11 LYD736 0.79 2.03E−02 3 44 LYD738 0.85 8.10E−042 28 LYD737 0.71 1.90E−03 1 6 LYD738 0.71 1.53E−02 2 48 LYD738 0.831.51E−03 2 20 LYD738 0.77 1.54E−02 9 1 LYD738 0.89 2.54E−04 2 14 LYD7380.74 5.56E−02 7 27 LYD738 0.79 1.08E−02 2 11 LYD738 0.70 1.10E−02 6 36LYD738 0.76 6.42E−03 5 40 LYD739 0.79 2.00E−03 4 25 LYD738 0.76 6.79E−033 48 LYD739 0.83 9.08E−04 4 15 LYD739 0.85 4.56E−04 4 4 LYD739 0.782.65E−03 4 3 LYD739 0.87 2.04E−04 4 7 LYD739 0.77 6.05E−03 4 8 LYD7390.87 2.76E−04 4 22 LYD739 0.75 7.69E−03 2 9 LYD739 0.75 4.93E−03 4 23LYD740 0.83 8.43E−04 1 21 LYD739 0.73 7.35E−03 4 6 LYD740 0.72 7.87E−031 1 LYD739 0.70 1.58E−02 2 37 LYD740 0.84 5.72E−04 4 14 LYD740 0.758.04E−04 1 35 LYD740 0.71 1.01E−02 9 25 LYD740 0.75 4.95E−03 4 28 LYD7400.72 8.55E−03 9 15 LYD740 0.75 4.87E−03 9 24 LYD740 0.70 1.05E−02 9 22LYD740 0.73 7.40E−03 9 7 LYD740 0.90 1.28E−04 9 8 LYD740 0.75 5.18E−03 948 LYD740 0.81 2.75E−03 5 24 LYD740 0.74 5.47E−03 9 3 LYD740 0.721.26E−02 5 35 LYD740 0.88 1.68E−04 9 6 LYD740 0.86 6.98E−04 5 7 LYD7400.82 2.11E−03 5 4 LYD740 0.78 4.92E−03 5 5 LYD740 0.86 6.11E−04 5 25LYD740 0.87 4.86E−04 5 3 LYD740 0.71 1.47E−02 5 30 LYD740 0.77 1.43E−025 8 LYD740 0.90 1.65E−04 5 22 LYD740 0.73 1.66E−02 5 11 LYD740 0.841.26E−03 5 23 LYD740 0.71 2.23E−02 7 35 LYD740 0.75 8.37E−03 5 6 LYD7400.74 1.51E−02 7 22 LYD740 0.77 9.67E−03 7 20 LYD740 0.77 8.79E−03 7 6LYD740 0.82 3.33E−03 7 7 LYD740 0.82 3.99E−03 7 13 LYD740 0.78 7.79E−037 3 LYD741 0.71 1.51E−02 2 18 LYD740 0.84 9.12E−03 7 11 LYD741 0.757.97E−03 5 41 LYD740 0.74 8.79E−03 3 46 LYD741 0.70 1.60E−02 5 40 LYD7410.73 1.04E−02 5 18 LYD741 0.77 2.47E−02 7 11 LYD741 0.77 7.03E−02 5 27LYD741 0.72 4.53E−02 3 44 LYD741 0.80 8.92E−03 7 1 LYD741 0.81 1.55E−026 1 LYD741 0.76 1.09E−02 7 13 LYD742 0.84 4.36E−03 2 11 LYD741 0.782.22E−02 6 21 LYD742 0.90 7.27E−05 9 24 LYD742 0.81 2.42E−03 2 19 LYD7420.81 1.46E−03 9 7 LYD742 0.74 5.90E−03 9 2 LYD742 0.76 3.91E−03 9 5LYD742 0.71 9.45E−03 9 25 LYD742 0.82 1.15E−03 9 23 LYD742 0.74 6.26E−039 12 LYD742 0.83 7.31E−04 9 13 LYD742 0.70 1.10E−02 9 3 LYD742 0.832.98E−03 7 18 LYD742 0.78 7.86E−03 9 11 LYD742 0.71 1.50E−02 3 20 LYD7420.71 2.13E−03 8 13 LYD742 0.72 1.18E−02 3 13 LYD742 0.75 8.10E−03 3 9LYD744 0.78 2.68E−03 9 32 LYD742 0.78 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7 14 LYD824 0.71 1.03E−02 9 40 LYD8230.87 1.21E−03 7 15 LYD824 0.86 1.46E−03 7 25 LYD823 0.79 7.05E−03 7 22LYD824 0.91 3.00E−04 7 5 LYD823 0.76 1.75E−02 7 8 LYD824 0.74 1.53E−02 722 LYD824 0.84 1.19E−03 9 8 LYD824 0.74 1.49E−02 7 23 LYD824 0.778.74E−03 7 24 LYD824 0.74 3.41E−02 7 11 LYD824 0.85 1.79E−03 7 7 LYD8250.71 1.52E−02 2 19 LYD824 0.74 1.38E−02 7 48 LYD825 0.73 1.09E−02 5 43LYD824 0.73 1.72E−02 7 3 LYD825 0.72 1.32E−02 5 31 LYD824 0.74 1.50E−027 6 LYD825 0.71 2.25E−03 8 5 LYD824 0.84 1.81E−02 6 44 LYD825 0.787.16E−03 7 40 LYD825 0.89 1.40E−03 2 11 LYD825 0.79 2.07E−02 3 11 LYD8250.83 1.58E−03 5 41 LYD826 0.84 1.12E−03 2 5 LYD825 0.75 1.27E−02 8 27LYD826 0.81 2.47E−03 5 41 LYD825 0.89 1.16E−03 7 8 LYD826 0.87 1.18E−027 27 LYD825 0.76 7.05E−03 3 48 LYD827 0.72 7.81E−03 4 43 LYD826 0.839.25E−04 4 19 LYD827 0.73 1.04E−02 2 18 LYD826 0.83 1.58E−03 5 43 LYD8270.81 5.02E−02 6 27 LYD826 0.87 2.54E−02 5 27 LYD828 0.78 3.43E−04 1 29LYD826 0.84 9.37E−03 3 44 LYD828 0.75 1.22E−02 7 18 LYD827 0.83 1.45E−034 44 LYD828 0.77 3.28E−03 6 26 LYD827 0.74 9.14E−02 5 27 LYD829 0.811.40E−04 1 48 LYD828 0.75 8.59E−04 1 41 LYD829 0.78 4.72E−03 3 25 LYD8280.82 2.02E−03 2 46 LYD830 0.79 4.08E−03 2 43 LYD828 0.87 4.62E−04 3 48LYD830 0.87 1.10E−03 2 44 LYD828 0.72 6.59E−02 6 8 LYD830 0.80 1.78E−039 33 LYD829 0.72 8.53E−03 9 12 LYD830 0.85 1.06E−03 5 41 LYD830 0.783.78E−02 4 27 LYD830 0.80 5.66E−03 7 14 LYD830 0.74 8.76E−03 2 41 LYD8300.80 3.15E−03 3 43 LYD830 0.77 3.15E−03 9 9 LYD830 0.84 8.85E−03 3 44LYD830 0.77 5.27E−03 5 43 LYD926 0.83 2.76E−03 2 44 LYD830 0.81 4.70E−037 2 LYD926 0.77 5.13E−03 5 33 LYD830 0.87 2.47E−03 7 1 LYD926 0.711.39E−02 3 28 LYD830 0.79 3.55E−03 3 41 LYD926 0.73 1.02E−02 3 6 LYD9260.82 1.79E−03 2 43 LYD929 0.77 6.08E−03 2 15 LYD926 0.87 5.46E−04 5 9LYD929 0.71 1.42E−02 2 22 LYD926 0.81 2.65E−02 7 27 LYD929 0.74 5.73E−039 37 LYD926 0.76 6.24E−03 3 48 LYD929 0.98 3.41E−07 5 41 LYD926 0.717.57E−02 6 44 LYD929 0.70 3.47E−02 7 1 LYD929 0.79 3.39E−02 2 27 LYD9290.77 4.08E−02 6 44 LYD929 0.80 3.27E−03 2 48 LYD930 0.73 1.14E−02 2 24LYD929 0.73 1.09E−02 2 3 LYD930 0.79 3.90E−03 2 25 LYD929 0.88 3.69E−045 43 LYD930 0.91 8.29E−05 2 15 LYD929 0.89 1.12E−03 5 44 LYD930 0.822.07E−03 2 22 LYD929 0.81 1.56E−02 6 21 LYD930 0.75 7.64E−03 2 6 LYD9300.72 1.51E−03 1 9 LYD930 0.74 6.45E−03 9 33 LYD930 0.85 8.97E−04 2 43LYD930 0.73 1.07E−02 5 32 LYD930 0.86 6.10E−04 2 41 LYD930 0.78 8.06E−037 2 LYD930 0.70 1.58E−02 2 17 LYD930 0.76 6.19E−03 3 48 LYD930 0.831.66E−03 2 3 MGP10 0.81 4.32E−03 7 25 LYD930 0.82 3.86E−03 2 44 MGP100.84 2.48E−03 7 5 LYD930 0.84 6.93E−04 9 10 MGP10 0.73 1.64E−02 7 48LYD930 0.87 2.01E−03 5 44 MGP10 0.75 1.20E−02 7 3 LYD930 0.72 2.01E−02 718 MGP10 0.90 1.40E−04 3 48 MGP10 0.78 4.91E−03 9 47 MGP10 0.86 3.18E−046 9 MGP10 0.85 1.84E−03 7 7 MGP10 0.90 4.33E−04 7 15 MGP10 0.81 4.41E−037 22 MGP10 0.77 8.50E−03 7 6 MGP10 0.71 9.58E−03 6 42 Provided are thecorrelations (R) between the expression levels yield improving genes andtheir homologs in various tissues [Expression (Exp) sets] and thephenotypic performance [yield, biomass, and plant architecture(Correlation vector (Cor))] under normal conditions across beanvarieties. P = p value.

Example 20 Production of B. Juncea Transcriptome and High ThroughputCorrelation Analysis with Yield Parameters Using 34K B. junceaOligonucleotide Micro-Arrays

In order to produce a high throughput correlation analysis, the presentinventors utilized a B. juncea oligonucleotide micro-array, produced byAgilent Technologies [chem. (dot) agilent (dot) com/Scripts/PDS (dot)asp?1Page=50879]. The array oligonucleotide represents about 34,000 B.juncea genes and transcripts. In order to define correlations betweenthe levels of RNA expression with yield components, various plantcharacteristics of 41 different B. juncea lines were analyzed and usedfor RNA expression analysis. The correlation between the RNA levels andthe characterized parameters was analyzed using Pearson correlationtest.

Correlation of B. juncea Genes' Expression Levels with PhenotypicCharacteristics Across Ecotype

Experimental Procedures

41 B. juncea varieties were grown in four repetitive plots, in field.Briefly, the growing protocol was as follows: B. juncea seeds were sownin soil and grown under normal conditions until harvest (fieldexperiment; normal growth conditions which included irrigation 2-3 timesa week, and fertilization given in the first month of the growthperiod). In order to define correlations between the levels of RNAexpression with yield components, 41 different B. juncea varieties wereanalyzed and used for gene expression analyses. Analysis was performedat flowering stage.

TABLE 159 B. juncea transcriptome expression sets Expression Set Set IDflower at pod setting stage under normal growth conditions 1 Leaf at podsetting stage under normal growth conditions 2 Pods and developing seedspod setting stage under normal 3 growth conditions stem at pod settingstage under normal growth conditions 4 Table 159.

RNA extraction—All 41 selected B. juncea varieties were sampled pertreatment. Plant tissues [fully expended leaf, stem, flowers and pods]growing under normal conditions were sampled and RNA was extracted asdescribed above.

The collected data parameters were as follows (summarized in Table 160):

Average shoot DW—Average weight of shoot per plant.

Average plant DW (Flowering) [g]—Average weight of all the plant atflowering (Stem DW+leaves DW).

Biomass per plant [Kg]—Average biomass at harvest above ground at drymature stage.

Grain yield [gr]—Seed weight per unit area.

Harvest index—Average seed yield per plant/Average dry weight.

Inflorescence height [cm]—Measure main raceme (Inflorescence) length.

Leaf area per plant [cm²]—Measurement was performed using a Leafarea-meter.

Leaves DW [gr]—Weight leaves after drying at flowering.

Number days 50% flowering [number]—Calculate days from day 1.

Number of reproductive lateral branches (Flowering) [number].

Plant height [cm]—Height of main stem measure from first node aboveground to last node before apex.

Plants number at harvest [number]—Count number of plants per plot.

Pod length [mm]—Measure lowest pods length.

Pods per main inflorescence [number]—Count number of pods on mainraceme.

Reproductive period [number]—Calculate number of days from bolting toharvest.

Relative growth rate [gr/day]—the relative growth rate (RGR) based ondry weight is calculated using Formula XXXIV above.

Seeds yield per plant [Kg]—Weight seeds per plot and normalized to 0%RH.

Specific leaf area (Flowering) [cm²/g]—Leaf area per gram leaf dryweight.

Stem DW (flowering) [gr]—Weight stem after drying at flowering.

Stem thickness [mm]—Measure Thickness of main branch base.

Experimental Results

41 different B. juncea varieties (i.e., Var1-41) were grown andcharacterized for 20 parameters as specified above. The average for eachof the measured parameters was calculated using the JMP software andvalues are summarized in Tables 161-165 below. Subsequent correlationanalysis between the various transcriptome expression sets and theaverage parameters was conducted. Results were then integrated to thedatabase (Table 166).

TABLE 160 B. juncea correlated parameters (vectors) Correlated parameterwith Correlation ID Avr Shoot DW [gr] 1 Avr plant DW (F) [gr] 2 Biomassper plant [kg] 3 Harvest index 4 Inflorescence height [cm] 5 Leaf areaper plant [cm²] 6 Leaves DW (flowering) [gr] 7 Num days 50% flowering 8Num of reproductive Lateral branches 9 Plant height [cm] 10 Plants numat harvest [number] 11 Pod length [mm] 12 Pods per main inflorescence[number] 13 Relative growth rate [gr/day] 14 Reproductive period[number] 15 Seeds yield per plant [kg] 16 Specific leaf area (F)[cm²/gr] 17 Stem DW (flowering) [gr] 18 Stem thickness [mm] 19 Grainyield [gr] 20 Table 160. “F” = Flowering. “Num” = number. “Avr” =average.

TABLE 161 Measured parameters in B. juncea varieties (lines 1-8)Ecotype/ Treatment Line-1 Line-2 Line-3 Line-4 Line-5 Line-6 Line-7Line-8 1 0.71 0.83 0.82 0.60 1.00 0.96 1.27 0.88 2 7.46 11.93 4.27 11.915.28 4.66 8.44 13.57 3 0.03 0.02 0.01 0.05 0.02 0.02 0.02 0.02 4 0.130.15 0.17 0.11 0.11 0.12 0.16 0.19 5 45.02 44.15 40.56 42.42 44.04 51.1357.92 47.94 6 811.00 587.00 472.10 406.75 335.36 391.62 454.50 777.75 75.45 4.65 4.75 3.85 4.30 5.19 4.45 8.32 8 39.00 32.50 32.00 32.67 26.0030.00 32.50 33.00 9 7.17 7.42 6.75 6.75 6.75 7.58 5.33 6.83 10 91.4290.79 100.23 103.06 58.65 86.02 98.56 109.42 11 165.75 193.50 231.0098.75 221.50 259.50 205.00 145.50 12 43.23 40.21 41.30 48.20 37.74 38.9543.77 45.51 13 35.71 34.75 26.38 14.78 27.63 31.46 31.58 28.38 14 0.170.19 0.13 0.16 0.18 0.17 0.22 0.17 15 52.00 58.50 71.00 62.67 58.0061.00 61.50 61.00 16 3.10 2.73 2.15 4.93 1.36 1.87 2.84 4.12 17 323.35402.48 300.95 307.41 244.34 242.62 308.33 300.53 18 16.93 31.14 8.0631.88 11.55 8.78 20.86 32.39 19 7.70 7.63 6.35 8.54 5.47 6.95 8.05 7.5520 550.50 572.75 516.75 517.50 330.00 526.25 608.00 616.00 Table 161.

TABLE 162 Measured parameters in B. juncea varieties (lines 9-16)Ecotype/ Line- Line- Line- Line- Line- Line- Line- Line- Treatment 9 1011 12 13 14 15 16 1 0.85 0.83 1.06 1.33 0.87 1.08 1.09 1.31 2 12.03 8.3511.19 10.80 7.84 9.11 11.69 5.43 3 0.02 0.02 0.03 0.02 0.02 0.03 0.020.02 4 0.15 0.17 0.13 0.16 0.15 0.12 0.17 0.18 5 42.58 32.41 31.34 47.0050.94 40.88 50.00 41.14 6 657.67 440.75 564.00 396.42 551.00 507.25765.17 552.16 7 4.80 3.87 6.25 3.85 3.45 3.92 5.25 6.51 8 NA NA 34.2532.00 32.50 33.75 32.50 26.50 9 6.83 6.08 7.00 5.92 5.42 5.83 6.25 7.0010 80.19 110.31 127.00 105.44 121.75 104.35 98.46 62.98 11 148.75 177.75193.50 176.25 210.75 189.50 223.75 222.00 12 42.74 36.30 34.44 45.7442.57 47.01 41.34 37.35 13 22.22 32.11 35.50 26.54 29.08 25.29 31.7927.75 14 0.23 0.18 0.21 0.23 0.17 0.18 0.21 0.19 15 NA NA 62.75 59.0064.50 60.25 64.50 67.25 16 2.95 3.33 2.57 3.61 2.94 2.66 2.81 2.78 17395.43 358.58 249.28 364.49 448.65 423.41 434.68 267.71 18 31.29 21.1827.33 28.56 20.08 23.40 29.81 11.41 19 7.05 9.65 7.84 8.08 8.59 7.457.09 5.66 20 462.75 648.50 527.50 607.25 666.50 534.00 681.00 556.75Table 162.

TABLE 163 Measured parameters in B. juncea varieties (lines 17-24)Ecotype/ Line- Line- Line- Line- Line- Line- Line- Line- Treatment 17 1819 20 21 22 23 24 1 0.82 1.04 0.95 1.42 1.16 1.08 0.76 1.06 2 4.75 6.1410.32 8.15 4.10 4.47 9.35 10.49 3 0.01 0.01 0.01 0.01 0.01 0.01 0.010.02 4 0.19 0.18 0.15 0.17 0.10 0.17 0.17 0.13 5 44.75 42.83 41.67 45.9047.11 39.64 46.38 40.42 6 374.51 694.62 657.67 234.75 405.43 470.64688.42 632.92 7 4.40 6.72 7.79 2.52 4.10 5.20 6.32 8.33 8 26.50 32.0031.50 30.33 31.00 31.00 33.75 31.50 9 5.25 7.75 6.67 5.50 6.17 6.25 7.587.17 10 67.48 97.56 90.65 90.06 82.49 96.47 89.77 131.83 11 220.75255.50 254.25 223.33 261.75 217.00 216.75 232.33 12 50.54 44.27 48.2850.36 49.56 50.65 43.43 35.63 13 23.83 25.28 22.42 24.53 27.13 23.2129.96 33.44 14 0.17 0.17 0.19 0.23 0.26 0.23 0.18 0.21 15 64.67 64.7558.50 64.33 46.00 65.50 59.75 59.00 16 2.46 2.46 2.07 2.42 1.30 2.462.68 2.25 17 252.49 319.29 253.13 252.16 300.97 290.18 327.41 234.17 189.87 11.70 23.16 21.94 8.19 8.22 21.74 23.12 19 6.40 7.19 7.27 7.98 6.836.95 7.66 8.71 20 581.75 668.50 561.00 574.00 360.75 478.67 626.50585.00 Table 163.

TABLE 164 Measured parameters in B. juncea varieties (lines 25-32)Ecotype/ Line- Line- Line- Line- Line- Line- Line- Line- Treatment 25 2627 28 29 30 31 32 1 0.84 1.06 1.20 1.17 0.97 0.86 0.98 1.18 2 9.54 10.725.21 6.71 9.34 5.64 11.58 4.55 3 0.02 0.01 0.02 0.01 0.02 0.01 0.01 0.014 0.13 0.18 0.15 0.18 0.18 0.20 0.17 0.11 5 42.58 45.25 50.29 42.5257.61 42.94 43.94 45.65 6 369.83 353.58 370.50 485.81 612.00 581.42427.00 463.19 7 3.40 2.70 2.87 5.07 6.38 4.42 3.61 5.16 8 31.67 30.5028.50 28.50 31.00 32.40 31.50 28.00 9 5.83 5.42 5.58 6.58 6.17 7.25 5.586.42 10 88.05 90.19 61.17 85.50 81.12 92.92 92.10 79.96 11 191.00 251.33212.25 225.00 175.00 243.17 263.75 240.75 12 42.30 39.88 39.10 45.9949.78 43.28 50.39 52.52 13 28.42 26.33 34.04 25.75 28.00 30.61 26.0025.79 14 0.16 0.24 0.26 0.22 0.17 0.19 0.15 0.20 15 65.17 53.00 65.0061.50 62.50 60.83 61.75 65.25 16 2.59 2.41 2.07 2.37 3.20 2.56 2.29 1.4417 342.65 395.55 376.46 286.95 282.95 385.46 358.73 266.19 18 25.2329.47 12.77 15.06 21.65 13.39 31.14 8.49 19 7.56 7.61 6.43 6.79 8.227.83 6.96 6.83 20 542.67 703.50 479.50 564.00 580.00 671.00 628.25378.75 Table 164.

TABLE 165 Measured parameters in B. juncea varieties (lines 33-41)Ecotype/ Line- Line- Line- Line- Line- Line- Line- Line- Line- Treatment33 34 35 36 37 38 39 40 41 1 1.22 1.33 0.74 0.93 1.08 0.99 0.98 1.270.65 2 7.74 6.36 6.52 8.42 14.27 6.45 9.53 12.55 9.49 3 0.01 0.01 0.030.02 0.02 0.01 0.02 0.01 0.03 4 0.17 0.19 0.10 0.20 0.18 0.18 0.16 0.150.18 5 44.76 48.54 49.81 45.60 46.22 47.89 34.23 48.13 51.75 6 416.58373.00 893.81 480.42 608.42 513.71 698.83 724.92 819.58 7 4.63 4.14 9.352.93 5.65 4.56 4.05 8.97 6.50 8 27.50 27.50 31.00 33.00 33.00 32.5034.00 30.50 NA 9 6.75 6.08 7.58 5.50 5.92 5.58 5.83 6.42 5.42 10 85.8377.79 81.81 115.75 90.61 82.67 143.75 92.69 148.63 11 210.00 227.25186.00 192.83 189.25 290.50 141.00 223.50 109.00 12 55.81 49.04 54.2943.09 47.41 47.21 31.18 48.49 35.43 13 24.92 28.21 39.87 33.06 24.8927.67 36.88 25.08 42.75 14 0.19 0.19 0.12 0.18 0.28 0.19 0.23 0.22 0.1715 65.75 62.50 75.50 70.00 70.00 58.00 69.00 62.75 NA 16 2.24 2.51 2.303.61 3.18 1.81 4.01 2.02 4.93 17 261.49 261.55 291.77 512.56 317.47323.08 353.77 242.76 370.04 18 18.59 14.93 10.22 22.34 37.15 14.81 24.5528.69 21.96 19 6.27 7.30 8.93 8.43 7.43 7.49 11.17 7.36 9.45 20 493.00601.25 438.75 747.17 661.00 550.25 487.25 483.25 570.50 Table 165.

TABLE 166 Correlation between the expression level of selected genes ofsome embodiments of the invention in various tissues and the phenotypicperformance under normal conditions across B. juncea varieties Corr.Gene Exp. Corr. Gene Exp. Set Name R P value set Set ID Name R P valueset ID LYD694 0.73 2.82E−04 1 17 LYD694 0.73 2.70E−04 3 19 LYD695 0.714.58E−04 1 17 LYD695 0.72 2.58E−04 2 20 LYD695 0.73 1.53E−04 2 17 Table166.

Example 21 Production of B. Juncea Transcriptome and High ThroughputCorrelation Analysis with Yield Parameters Using 60K B. JunceaOligonucleotide Micro-Arrays

In order to produce a high throughput correlation analysis, the presentinventors utilized a B. juncea oligonucleotide micro-array, produced byAgilent Technologies [chem. (dot) agilent (dot) com/Scripts/PDS (dot)asp?1Page=50879]. The array oligonucleotide represents about 60,000 B.juncea genes and transcripts. In order to define correlations betweenthe levels of RNA expression with yield components or vigor relatedparameters, various plant characteristics of 11 different B. junceavarieties were analyzed and used for RNA expression analysis. Thecorrelation between the RNA levels and the characterized parameters wasanalyzed using Pearson correlation test.

Correlation of B. juncea Genes' Expression Levels with PhenotypicCharacteristics Across Ecotype

Experimental Procedures

11 B. juncea varieties were grown in three repetitive plots, in field.Briefly, the growing protocol was as follows: B. juncea seeds were sownin soil and grown under normal condition till harvest [field experiment,normal growth conditions which included irrigation 2-3 times a week with861 m³ water per dunam (1000 square meters) per entire growth period,and fertilization of 12 units of nitrogen given in the first month ofthe growth period]. In order to define correlations between the levelsof RNA expression with yield components or vigor related parameters, the11 different B. juncea varieties were analyzed and used for geneexpression analyses.

TABLE 167 Tissues used for B, juncea transcriptome expression setsExpression Description Set Pod (R4-R5) under normal growth conditions 1Flower at flowering stage under normal growth conditions 2 Pod (R4-R5)under normal growth conditions 3 Meristem at vegetative stage undernormal growth 4 conditions Leaf at vegetative stage under normal growthconditions 5 Table 167: Provided are the identification (ID) digits ofeach of the B, juncea expression sets.

RNA extraction—All 11 selected B. juncea varieties were sample per eachtreatment. Plant tissues [leaf, Pod, Lateral meristem and flower]growing under normal conditions were sampled and RNA was extracted asdescribed above.

The collected data parameters were as follows:

Fresh weight (plot-harvest) [gr/plant]—total fresh weight per plot atharvest time normalized to the number of plants per plot.

Seed Weight [milligrams/plant]—total seeds from each plot was extracted,weighted and normalized for plant number in each plot.

Harvest index—The harvest index was calculated: seed weight/freshweight.

Days till bolting/flowering—number of days till 50% bolting/floweringfor each plot.

SPAD—Chlorophyll content was determined using a Minolta SPAD 502chlorophyll meter and measurement was performed at time of flowering.SPAD meter readings were done on young fully developed leaf. Threemeasurements per leaf were taken for each plot.

Main branch-average node length—total length/total number of nods onmain branch.

Lateral branch-average node length—total length/total number of nods onlateral branch.

Main branch-20th length—the length of the pod on the 20^(th) node fromthe apex of main branch.

Lateral branch-20th length—the length of the pod on the 20^(th) nodefrom the apex of lateral branch.

Main branch-20th seed No.—number of seeds in the pod on the 20^(th) nodefrom the apex of main branch.

Lateral branch-20th seed number—number of seeds in the pod on the20^(th) node from the apex of lateral branch.

Number of lateral branches—total number of lateral branches, average ofthree plants per plot.

Main branch height [cm]—total length of main branch.

Min-lateral branch position—lowest node on the main branch that hasdeveloped lateral branch.

Max-lateral branch position [#node of main branch]—highest node on themain branch that has developed lateral branch.

Max-number of nodes in lateral branch—the highest number of node that alateral branch had per plant.

Max length of lateral branch [cm]—the highest length of lateral branchper plant.

Max diameter of lateral branch [mm]—the highest base diameter that alateral branch had per plant.

Oil Content—Indirect oil content analysis was carried out using NuclearMagnetic Resonance (NMR) Spectroscopy, which measures the resonanceenergy absorbed by hydrogen atoms in the liquid state of the sample [Seefor example, Conway T F. and Earle F R., 1963, Journal of the AmericanOil Chemists' Society; Springer Berlin/Heidelberg, ISSN: 0003-021X(Print) 1558-9331 (Online)];

Fresh weight (single plant) (gr/plant)—average fresh weight of threeplants per plot taken at the middle of the season.

Main branch base diameter [mm]—the based diameter of main branch,average of three plants per plot.

1000 Seeds [gr]—weight of 1000 seeds per plot.

Experimental Results

Eleven different B. juncea varieties were grown and characterized for 23parameters as specified above and summarized in Table 168. The averagefor each of the measured parameters was calculated using the JMPsoftware and values are summarized in Tables 169-170 below. Subsequentcorrelation analysis between the various transcriptome expression setsand the average parameters was conducted. Results were then integratedto the database (Table 171).

TABLE 168 Measured parameters in B, juncea accessions CorrelationCorrelated parameter with ID 1000 Seeds [gr.] 1 Days till bolting (days)2 Days till flowering (days) 3 Fresh weight (plot-harvest) [gr./plant] 4Fresh weight (single plant) [gr./plant] 5 Harvest index (ratio) 6Lateral branch - 20th length (cm) 7 Lateral branch - 20th seed number(number) 8 Lateral branch - average node length (cm) 9 Main branch -20th length (cm) 10 Main branch - 20th seed number (number) 11 Mainbranch - average node length (cm) 12 Main branch base diameter [mm] 13Main branch height [cm] 14 Max-Diameter of lateral branch [mm] 15Max-Lateral branch position [# node of main 16 branch] Max-Length oflateral branch [cm] 17 Max-Number of nodes in lateral branch (number) 18Min-Lateral branch position (#node of main 19 branch) Number of lateralbranches (number) 20 Oil content (mg) 21 SPAD 22 Seed weight per plant(gr.) 23 Table 168. Provided are the B, juncea correlated parameters.“gr.” = grams; mm = millimeters; “cm” = centimeters; “mg” = milligrams;“SPAD” = chlorophyll levels; “#” = number.

TABLE 169 Measured parameters in B. juncea accessions (lines 1-6)Ecotype/ Treatment Line-1 Line-2 Line-3 Line-4 Line-5 Line-6 1 3.76 2.213.26 2.36 2.00 3.12 2 57.33 60.33 59.67 56.33 55.00 46.67 3 66.00 69.6769.33 66.00 61.33 53.00 4 69.24 45.22 39.27 49.11 43.95 46.42 5 197.78142.22 147.22 243.33 192.33 163.78 6 0.00006 0.00013 0.00014 0.000140.00013 0.00014 7 4.32 3.69 4.14 3.37 3.06 3.96 8 13.00 14.00 13.2213.44 11.00 13.11 9 0.65 0.43 0.74 0.57 0.56 0.79 10 4.28 3.72 3.62 3.502.74 5.20 11 13.22 13.67 10.44 14.11 9.78 15.22 12 0.48 0.41 0.63 0.430.38 0.68 13 14.53 11.99 19.91 14.32 12.59 12.30 14 140.72 125.22 112.44133.39 142.00 101.50 15 4.20 4.85 4.34 5.74 5.87 5.68 16 15.22 14.8913.56 14.89 14.00 10.89 17 40.44 47.22 41.61 60.50 59.78 59.44 18 5.227.00 5.22 7.00 6.56 9.44 19 6.78 6.33 5.56 3.67 3.00 3.11 20 15.22 14.8913.56 14.89 14.00 9.78 21 40.19 40.71 40.91 38.57 40.14 42.63 22 33.0230.01 32.83 37.53 41.44 35.41 23 0.00438 0.00572 0.00553 0.00687 0.005810.00628 Table 169.

TABLE 170 Measured parameters in B. juncea accessions (lines 7-11)Ecotype/ Treatment Line-7 Line-8 Line-9 Line-10 Line-11 1 3.34 3.09 3.393.40 2.39 2 59.00 54.33 59.67 57.33 53.00 3 69.67 63.67 69.67 71.0058.33 4 36.14 32.58 33.16 63.23 60.94 5 164.44 181.11 176.22 217.89261.11 6 0.00013 0.00013 0.00014 0.00009 0.00012 7 4.33 4.21 4.14 4.043.88 8 11.89 13.44 11.22 13.22 14.00 9 0.57 0.76 0.96 0.78 0.90 10 3.913.98 3.46 3.73 4.04 11 12.00 12.67 9.89 11.56 15.56 12 0.40 0.63 0.570.59 1.55 13 12.60 12.91 12.56 13.77 13.56 14 145.39 131.56 129.89131.56 116.44 15 4.52 4.89 4.68 5.56 5.49 16 16.44 14.33 14.56 14.1116.78 17 47.28 47.33 44.67 58.67 47.17 18 6.11 5.22 5.67 6.56 6.00 197.78 6.22 5.56 4.89 5.33 20 16.44 14.33 14.56 14.11 16.78 21 41.34 40.8240.82 38.14 37.21 22 33.17 32.87 34.80 31.82 41.49 23 0.00458 0.004370.00448 0.00566 0.00706 Table 170: Provided are the values of each ofthe parameters (as described above) measured in B. juncea accessions(Seed ID) under normal conditions.

TABLE 171 Correlation between the expression level of selected genes ofsome embodiments of the invention in various tissues and the phenotypicperformance under normal or normal conditions across B. Junceaaccessions Gene Exp. Corr. Gene Exp. Corr. Name R P value set Set IDName R P value set Set ID LGP19 0.72 2.85E−02 4 4 LGP19 0.74 9.33E−02 29 LGP19 0.76 6.77E−03 1 9 LGP45 0.76 7.92E−02 2 15 LGP45 0.75 8.72E−02 25 LGP45 0.87 2.55E−02 2 23 LGP45 0.86 2.68E−02 2 4 LYD694 0.72 2.83E−024 5 LYD694 0.73 2.56E−02 4 4 LYD694 0.73 1.01E−01 2 4 LYD694 0.702.33E−02 5 1 LYD694 0.72 1.21E−02 1 12 LYD695 0.95 4.06E−03 2 22 LYD6960.96 8.60E−03 1 9 LYD696 0.97 7.40E−03 1 12 Table 171. Provided are thecorrelations (R) between the expression levels of yield improving genesand their homologues in tissues [Leaves, meristem, flower and pods;Expression sets (Exp)] and the phenotypic performance in various yield,biomass, growth rate and/or vigor components [Correlation vector(corr.)] under stress conditions or normal conditions across B, junceaaccessions. P = p value.

Example 22 Gene Cloning and Generation of Binary Vectors for PlantExpression

To validate their role in improving yield, selected genes wereover-expressed in plants, as follows.

Cloning Strategy

Selected genes from those presented in Examples 1-21 hereinabove werecloned into binary vectors for the generation of transgenic plants. Forcloning, the full-length open reading frames (ORFs) were identified. ESTclusters and in some cases mRNA sequences were analyzed to identify theentire open reading frame by comparing the results of severaltranslation algorithms to known proteins from other plant species.

In order to clone the full-length cDNAs, reverse transcription (RT)followed by polymerase chain reaction (PCR; RT-PCR) was performed ontotal RNA extracted from leaves, roots or other plant tissues, growingunder normal/limiting or stress conditions. Total RNA extraction,production of cDNA and PCR amplification was performed using standardprotocols described elsewhere (Sambrook J., E. F. Fritsch, and T.Maniatis. 1989. Molecular Cloning. A Laboratory Manual, 2nd Ed. ColdSpring Harbor Laboratory Press, New York) which are well known to thoseskilled in the art. PCR products were purified using PCR purificationkit (Qiagen).

Usually, 2 sets of primers were prepared for the amplification of eachgene, via nested PCR (if required). Both sets of primers were used foramplification on a cDNA. In case no product was obtained, a nested PCRreaction was performed. Nested PCR was performed by amplification of thegene using external primers and then using the produced PCR product as atemplate for a second PCR reaction, where the internal set of primerswere used. Alternatively, one or two of the internal primers were usedfor gene amplification, both in the first and the second PCR reactions(meaning only 2-3 primers are designed for a gene). To facilitatefurther cloning of the cDNAs, an 8-12 base pairs (bp) extension wasadded to the 5′ of each internal primer. The primer extension includesan endonuclease restriction site. The restriction sites were selectedusing two parameters: (a) the restriction site does not exist in thecDNA sequence; and (b) the restriction sites in the forward and reverseprimers were designed such that the digested cDNA was inserted in thesense direction into the binary vector utilized for transformation.

PCR products were digested with the restriction endonucleases (NewEngland BioLabs Inc) according to the sites designed in the primers.Each digested/undigested PCR product was inserted into a high copyvector pUC19 (New England BioLabs Inc], or into plasmids originatingfrom this vector. In some cases the undigested PCR product was insertedinto pCR-Blunt II-TOPO (Invitrogen) or into pJET1.2 (CloneJET PCRCloning Kit, Thermo Scientific) or directly into the binary vector. Thedigested/undigested products and the linearized plasmid vector wereligated using T4 DNA ligase enzyme (Roche, Switzerland or othermanufacturers). In cases where pCR-Blunt II-TOPO is used no T4 ligase isneeded.

Sequencing of the inserted genes was performed, using the ABI 377sequencer (Applied Biosystems). In some cases, after confirming thesequences of the cloned genes, the cloned cDNA was introduced into amodified pGI binary vector containing the At6669 promoter (e.g., pQFNc)and the NOS terminator (SEQ ID NO: 15762) via digestion with appropriaterestriction endonucleases.

In case of Brachypodium transformation, after confirming the sequencesof the cloned genes, the cloned cDNAs were introduced into pEBbVNi (FIG.9A) containing 35S promoter (SEQ ID NO: 15763) and the NOS terminator(SEQ ID NO: 15762) via digestion with appropriate restrictionendonucleases. The genes were cloned downstream to the 35S promoter andupstream to the NOS terminator.

Several DNA sequences of the selected genes were synthesized by GeneArt(Life Technologies, Grand Island, N.Y., USA). Synthetic DNA was designedin silico. Suitable restriction enzymes sites were added to the clonedsequences at the 5′ end and at the 3′ end to enable later cloning intothe desired binary vector.

Binary vectors—The pPI plasmid vector was constructed by inserting asynthetic poly-(A) signal sequence, originating from pGL3 basic plasmidvector (Promega, GenBank Accession No. U47295; nucleotides 4658-4811)into the HindIII restriction site of the binary vector pBI101.3(Clontech, GenBank Accession No. U12640). pGI is similar to pPI, but theoriginal gene in the backbone is GUS-Intron and not GUS.

The modified pGI vector (e.g., pQFN, pQFNc, pQYN_6669, pQNa_RP, pQFYN orpQXNc) is a modified version of the pGI vector in which the cassette isinverted between the left and right borders so the gene and itscorresponding promoter are close to the right border and the NPTII geneis close to the left border.

At6669, the new Arabidopsis thaliana promoter sequence (SEQ ID NO:15751) was inserted in the modified pGI binary vector, upstream to thecloned genes, followed by DNA ligation and binary plasmid extractionfrom positive E. coli colonies, as described above. Colonies wereanalyzed by PCR using the primers covering the insert which weredesigned to span the introduced promoter and gene. Positive plasmidswere identified, isolated and sequenced.

pEBbVNi (FIG. 9A) is a modified version of pJJ2LB in which theHygromycin resistance gene was replaced with the BAR gene which confersresistance to the BASTA herbicide [BAR gene coding sequence is providedin GenBank Accession No. JQ293091.1 (SEQ ID NO: 15764); furtherdescription is provided in Akama K, et al. “EfficientAgrobacterium-mediated transformation of Arabidopsis thaliana using thebar gene as selectable marker”, Plant Cell Rep. 1995, 14(7):450-4;Christiansen P, et al. “A rapid and efficient transformation protocolfor the grass Brachypodium distachyon”, Plant Cell Rep. 2005 March;23(10-11):751-8. Epub 2004 Oct. 19; and P{hacek over (a)}curar D I, etal. “A high-throughput Agrobacterium-mediated transformation system forthe grass model species Brachypodium distachyon L”, Transgenic Res. 200817(5):965-75; each of which is fully incorporated herein by reference inits entirety]. The pEBbVNi construct contains the 35S promoter (SEQ IDNO: 15763). pJJ2LB is a modified version of pCambia0305.2 (Cambia).

In case genomic DNA was cloned, the genes were amplified by direct PCRon genomic DNA extracted from leaf tissue using the DNAeasy kit (QiagenCat. No. 69104).

Selected genes cloned by the present inventors are provided in Table 172below.

TABLE 172 Cloned genes Gene Polynucleotide Polypeptide SEQ ID Name Highcopy plasmid Organism Primers used SEQ ID NOs: SEQ ID NO: NO: LGP1pUCsFN_LGP1 ARABIDOPSIS Arabidopsis thalia 16135, 15859, 16114, 15809395 713 LGP10 pUCsFN_LGP10 ARABIDOPSIS Arabidopsis thalia 16027, 15820,16040, 15855 400 718 LGP100 pMA_LGP100_GA 466 786 LGP101 pUC19c_LGP101RICE Oryza sativa L. 15800, 16288, 16466, 16204 467 787 LGP102pMK_LGP102_GA 468 788 LGP103 pUC19c_LGP103 SORGHUM Sorghum bicolor16051, 16215, 16072, 16335 469 1090 LGP104 pQFNc_LGP104 SOYBEAN Glycinemax 16015, 15832, 16181, 15858 470 790 LGP105 pUC19c_LGP105 SOYBEANGlycine max 16001, 16334, 16001, 16334 471 791 LGP106 TopoB_LGP106SOYBEAN Glycine max 16139, 15853, 16073, 15849 472 792 LGP107 pMA- 473793 RQ_LGP107_GA LGP108 pUC19_LGP108 WHEAT Triticum aestivum L. 16424,15895, 16424, 15895 474 1091 LGP109 pUC19c_LGP109 SOYBEAN Glycine max16003, 15802, 16034, 15846 475 1092 LGP12 pUCsFN_LGP12 ARABIDOPSISArabidopsis thalia 15969, 15810, 15945, 16472 401 719 LGP18pUC57_LGP18_GA 402 720 LGP19 pUCsFN_LGP19 MUSTARD Brassica juncea 15861,15911, 15861, 15907 403 1067 LGP20 pUCsFN_LGP20 BARLEY Hordeum vulgareL. 16058, 16471, 16058, 16469 404 1068 LGP21 pUCsFN_LGP21 BARLEY Hordeumvulgare L. 16375, 16477, 16383, 15932 405 723 LGP22 pUCsFN_LGP22 BARLEYHordeum vulgare L. 15836, 15864, 15836, 15864 406 724 LGP24 pUC19c_LGP24lettuce 16173, 16308, 15934, 16242 407 725 LGP25 pUCsFN_LGP25 MAIZE Zeamays L. 16037, 16470, 15963, 15860 408 1069 LGP27 pUC19c_LGP27 MAIZE Zeamays L. 16024, 16219, 15982, 16189 409 1070 LGP3 pUCsFN_LGP3 ARABIDOPSISArabidopsis thalia 16410, 16172, 16410, 16172 396 714 LGP32 pUCsFN_LGP32TOMATO Lycopersicum esculentum 16153, 15818, 15961, 15814 410 728 LGP34pUCsFN_LGP34 TOMATO Lycopersicum esculentum 15960, 15869, 16099, 15869411 729 LGP35 pUC19c_LGP35 TOMATO Lycopersicum esculentum 16079, 16225,16081, 16318 412 1071 LGP38 pUC57_LGP38_GA 413 731 LGP39 pUC57_LGP39_GA414 732 LGP41 pUC57_LGP41_GA 415 733 LGP42 pUC19c_LGP42 TOMATOLycopersicum esculentum 16120, 16196, 15940, 16247 416 1072 LGP43pUCsFN_LGP43 CANOLA Brassica napus 16409, 16029, 16409, 16029 417 735LGP44 pUCsFN_LGP44 ARABIDOPSIS Arabidopsis thalia 16025, 15829, 15953,15823 418 736 LGP45 pUCsFN_LGP45 MUSTARD Brassica juncea 16076, 15826,15996, 15804 419 737 LGP46 pUCsFN_LGP46 ARABIDOPSIS Arabidopsis thalia16394, 15918, 16456, 15924 420 738 LGP47 pUCsFN_LGP47 COTTON Gossypiumhirsutum 16036, 16467, 16125, 16473 421 1073 LGP48 pUCsFN_LGP48 CANOLABrassica napus 15933, 16344, 16151, 16344 422 1074 LGP49 pUCsFN_LGP49CANOLA Brassica napus 16448, 15783, 16448, 15769 423 741 LGP52pUCsFN_LGP52 SORGHUM Sorghum bicolor 16454, 15885, 16441, 15904 424 742LGP53 pUCsFN_LGP53 ARABIDOPSIS Arabidopsis thalia 15946, 15828, 16134,15850 425 743 LGP54 pUCsFN_LGP54 CANOLA Brassica napus 16046, 16217,16048, 16202 426 744 LGP58 pUCsFN_LGP58 COTTON Gossypium hirsutum 16170,15831, 16170, 15831 427 1075 LGP59 pMA-RQ_LGP59_GA 428 746 LGP6pUCsFN_LGP6 ARABIDOPSIS Arabidopsis thalia 15942, 15837, 16096, 16474397 715 LGP60 pMA_LGP60_GA 429 747 LGP61 pMA-RQ_LGP61_GA 430 748 LGP62pMA-RQ_LGP62_GA 431 749 LGP63 pMS-RQ_LGP63_GA 432 750 LGP64pMA-RQ_LGP64_GA 433 751 LGP65 pUC19c_LGP65 COTTON Gossypium hirsutum16451, 15884, 16402, 15906 434 752 LGP66 pQFNc_LGP66 PHYSCOMITRELLAPhyscomitrella 16427, 15916, 16427, 15916 435 1076 LGP67 pQFNc_LGP67CANOLA Brassica napus 16019, 16188, 16019, 16193 436 1077 LGP68pMA-RQ_LGP68_GA 437 755 LGP69 pUC19c_LGP69 CANOLA Brassica napus 15970,16227, 16086, 16261 438 1078 LGP71 pUCsFN_LGP71 Phaseolus vulgaris16137, 16294, 16108, 16236 439 757 LGP72 TopoB_LGP72 MAIZE Zea mays L.16435, 15791, 16423, 16482 440 1079 LGP73 pMA-T_LGP73_GA 441 759 LGP74pMA-T_LGP74_GA 442 760 LGP75 pUCsFN_LGP75 MAIZE Zea mays L. 16390,15768, 16398, 15766 443 761 LGP76 pUCsFN_LGP76 RICE Oryza sativa L.16087, 15803, 16087, 15803 444 762 LGP77 pMA-T_LGP77_GA 445 763 LGP78pUCsFN_LGP78 SOYBEAN Glycine max 15993, 15812, 16016, 15844 446 764LGP79 pUCsFN_LGP79 SOYBEAN Glycine max 16160, 15808, 16100, 15841 4471080 LGP8 pUCsFN_LGP8 ARABIDOPSIS Arabidopsis thalia 15956, 15835,16056, 15857 398 716 LGP80 pUCsFN_LGP80 MAIZE Zea mays L. 16376, 15784,16376, 15784 448 1081 LGP81 pUCsFN_LGP81 SOYBEAN Glycine max 16436,15771, 16420, 15790 449 767 LGP82 pUCsFN_LGP82 MAIZE Zea mays L. 15821,15865, 15807, 15880 450 768 LGP83 pUC19c_LGP83 BARLEY Hordeum vulgare L.16021, 15840, 16021, 15822 451 769 LGP84 pQFNc_LGP84 Phaseolus vulgaris16411, 15775, 16411, 15775 452 1082 LGP85 pUC19c_LGP85 Phaseolusvulgaris 16460, 16462, 16461, 16462 453 1083 LGP86 pMA-RQ_LGP86_GA 454772 LGP87 pQFNc_LGP87 MAIZE Zea mays L. 16430, 16476, 16452, 15923 455773 LGP88 pQFNc_LGP88 MAIZE Zea mays L. 15917, 15897, 15917, 15897 4561084 LGP89 pQFNc_LGP89 MAIZE Zea mays L. 16085, 16468, 16085, 16468 4571085 LGP9 pUCsFN_LGP9 ARABIDOPSIS Arabidopsis thalia 15862, 15796,15847, 16464 399 717 LGP90 pUC19c_LGP90 MAIZE Zea mays L. 16379, 15874,16379, 15874 458 1086 LGP91 pQFNc_LGP91 MAIZE Zea mays L. 16127, 16481,16011, 16483 459 1087 LGP94 pUC19c_LGP94 MAIZE Zea mays L. 16006, 15851,16109, 15830 460 780 LGP95 pMA_LGP95_GA 461 781 LGP96 pUC19c_LGP96Medicago 15972, 16304, 16078, 16304 462 1088 LGP97 pMA_LGP97_GA 463 783LGP98 pMA_LGP98_GA 464 784 LGP99 pUC19c_LGP99 RICE Oryza sativa L.16111, 15845, 16004, 15815 465 1089 LYD237 pMA-RQ_MGP14_GA 477 797LYD694 pMA-T_LYD694_GA 489 809 LYD695 pUC19c_LYD695 Brassica Juncea15935, 16201, 15935, 16201 490 810 LYD696 pQFNc_LYD696 Brassica Juncea16084, 16325, 16084, 16325 491 1094 LYD698 pMA-T_LYD698_GA 492 812LYD699 pMA-T_LYD699_GA 493 813 LYD700 pMA-T_LYD700_GA 494 814 LYD701pQFNc_LYD701 Phaseolus vulgaris 16028, 16191 495 815 LYD702 pUC19_LYD702Phaseolus vulgaris 16103, 16220 496 816 LYD703 pMA-T_LYD703_GA 497 817LYD704 pUC19c_LYD704 Phaseolus vulgaris 16150, 16327, 16069, 16298 498818 LYD705 pQFNc_LYD705 Phaseolus vulgaris 16032, 16289 499 819 LYD706pUC19_LYD706 Phaseolus vulgaris 15801, 15834, 15798, 15816 500 1095LYD707 pQFNc_LYD707 Phaseolus vulgaris 15848, 15795, 15819, 16465 501821 LYD708 pQFNc_LYD708 Phaseolus vulgaris 16131, 16246, 16131, 16246502 822 LYD710 pMA-T_LYD710_GA 503 823 LYD711 pQFNc_LYD711 Phaseolusvulgaris 16414, 15973, 16385, 16063 504 1096 LYD713 pUC19c_LYD713Phaseolus vulgaris 16133, 16186, 15977, 16312 505 825 LYD714pQFNc_LYD714 Phaseolus vulgaris 16162, 16319, 16039, 16322 506 826LYD715 pMA-T_LYD715_GA 507 827 LYD717 pQFNc_LYD717 Phaseolus vulgaris16026, 16258, 16026, 16258 508 828 LYD718 pUC19c_LYD718 Phaseolusvulgaris 16023, 16205, 16121, 16210 509 1097 LYD719 pQFNc_LYD719Phaseolus vulgaris 15928, 16292, 15928, 16303 510 830 LYD720pQFNc_LYD720 Phaseolus vulgaris 16372, 15908 511 831 LYD721 pQFNc_LYD721Phaseolus vulgaris 15817, 15793, 15817, 15793 512 1098 LYD722pQFNc_LYD722 Phaseolus vulgaris 16388, 16145, 16412, 16145 513 1099LYD723 pQFNc_LYD723 Phaseolus vulgaris 15990, 15909, 15990, 15909 514834 LYD725 pQFNc_LYD725 Phaseolus vulgaris 16075, 16300 515 1100 LYD726pMA-T_LYD726_GA 516 836 LYD727 pUC19c_LYD727 Phaseolus vulgaris 16035,16207, 15980, 16293 517 837 LYD729 pMA-T_LYD729_GA 518 838 LYD730pUC19c_LYD730 Phaseolus vulgaris 16399, 15875, 16450, 15867 519 839LYD731 pQFNc_LYD731 Phaseolus vulgaris 15978, 16321, 16148, 16341 520840 LYD733 pQFNc_LYD733 Phaseolus vulgaris 16419, 15899 521 841 LYD735pMA-T_LYD735_GA 522 842 LYD737 pQFNc_LYD737 Phaseolus vulgaris 16429,15892, 16429, 15892 523 844 LYD738 pQFNc_LYD738 Phaseolus vulgaris16140, 16342, 16060, 16198 524 1101 LYD739 pQFNc_LYD739 Phaseolusvulgaris 16130, 16281, 16118, 16276 525 846 LYD740 pQFNc_LYD740Phaseolus vulgaris 16431, 15903, 16443, 15890 526 847 LYD741TopoB_LYD741 Phaseolus vulgaris 16045, 16309, 16045, 16309 527 848LYD742 pQFNc_LYD742 Phaseolus vulgaris 15984, 16199, 16128, 16317 5281102 LYD744 pUC19_LYD744 Phaseolus vulgaris 15805, 15913, 15813, 15913529 1103 LYD745 pMA-T_LYD745_GA 530 851 LYD746 pMA-T_LYD746_GA 531 852LYD747 pMA_LYD747_GA 532 853 LYD748 pQFNc_LYD748 Phaseolus vulgaris16062, 16274, 15950, 16234 533 1104 LYD749 pMA-T_LYD749_GA 534 855LYD750 pQFNc_LYD750 Phaseolus vulgaris 16152, 16184, 15966, 16347 535856 LYD751 pQFNc_LYD751 Phaseolus vulgaris 16449, 16052, 16433, 16050536 857 LYD752 TopoB_LYD752 Phaseolus vulgaris 16439, 15866 537 858LYD753 pUC19c_LYD753 Phaseolus vulgaris 15986, 16356, 16053, 16345 5381105 LYD754 pQFNc_LYD754 Phaseolus vulgaris 16041, 16187, 15958, 16229539 860 LYD755 pQFNc_LYD755 Phaseolus vulgaris 15926, 16248, 16174,16223 540 861 LYD756 pQFNc_LYD756 Phaseolus vulgaris 16090, 16297,16093, 16299 541 862 LYD757 pQFNc_LYD757 Phaseolus vulgaris 16168,16240, 15955, 16363 542 863 LYD758 pUC19c_LYD758 Phaseolus vulgaris16407, 15773, 16407, 15773 543 1106 LYD760 pQFNc_LYD760 Phaseolusvulgaris 16095, 16251, 16095, 16365 544 1107 LYD761 pQFNc_LYD761Phaseolus vulgaris 16180, 16316 545 866 LYD762 pUC19c_LYD762 Phaseolusvulgaris 16013, 16306, 15974, 16296 546 867 LYD763 pUC19c_LYD763Phaseolus vulgaris 15929, 16185, 16147, 16249 547 1108 LYD764pQFNc_LYD764 Phaseolus vulgaris 16403, 15898, 16422, 15887 548 1109LYD765 pUC19_LYD765 Phaseolus vulgaris 16382, 15787, 16386, 15788 5491110 LYD767 pQFNc_LYD767 Phaseolus vulgaris 16070, 16228, 16124, 16282550 871 LYD768 pUC19_LYD768 Phaseolus vulgaris 16123, 16357, 16123,16357 551 1111 LYD769 pMA-T_LYD769_GA 552 873 LYD771 pUC19c_LYD771Phaseolus vulgaris 16179, 16305, 15927, 16311 553 1112 LYD772pQFNc_LYD772 Phaseolus vulgaris 16017, 16230, 16017, 16218 554 1113LYD773 pMA-T_LYD773_GA 555 876 LYD774 pQFNc_LYD774 Phaseolus vulgaris16175, 16280, 16110, 16266 556 877 LYD776 pQFNc_LYD776 Phaseolusvulgaris 16038, 16367, 16155, 16244 557 878 LYD777 pQFNc_LYD777Phaseolus vulgaris 16098, 16337, 16122, 16192 558 879 LYD778TopoB_LYD778 Phaseolus vulgaris 16054, 16206, 15983, 16232 559 1114LYD779 pQFNc_LYD779 Phaseolus vulgaris 15827, 15777, 15827, 15770 5601115 LYD780 pUC19_LYD780 Phaseolus vulgaris 15994, 16253, 16158, 16364561 882 LYD781 pQFNc_LYD781 Phaseolus vulgaris 16101, 16290, 16101,16268 562 1116 LYD782 pQFNc_LYD782 Phaseolus vulgaris 16178, 16352,16163, 16336 563 1117 LYD783 pMA_LYD783_GA 564 885 LYD784pMK-T_LYD784_GA 565 886 LYD785 TopoB_LYD785 Phaseolus vulgaris 16154,16286, 15998, 16353 566 887 LYD786 pUC19_LYD786 Phaseolus vulgaris15981, 16348 567 888 LYD788 pUC19c_LYD788 Phaseolus vulgaris 16373,15871, 16373, 15882 568 889 LYD789 pMA-T_LYD789_GA 569 890 LYD790pQFNc_LYD790 Phaseolus vulgaris 16043, 16275, 15991, 16275 570 1118LYD791 TopoB_LYD791 Phaseolus vulgaris 16018, 16273, 16042, 16260 571892 LYD792 pUC19c_LYD792 Phaseolus vulgaris 16445, 15778, 16444, 15794572 1119 LYD793 pQFNc_LYD793 Phaseolus vulgaris 16459, 15792, 16459,15782 573 1120 LYD794 pQFNc_LYD794 Phaseolus vulgaris 16057, 16264,16057, 16264 574 895 LYD795 pUC19_LYD795 Phaseolus vulgaris 16171,16287, 16119, 16257 575 896 LYD796 pUC19c_LYD796 Phaseolus vulgaris16141, 16233, 16141, 16233 576 897 LYD798 pQFNc_LYD798 Phaseolusvulgaris 16377, 15954, 16393, 16055 577 1121 LYD799 pQFNc_LYD799Phaseolus vulgaris 16446, 15919, 16446, 15919 578 1122 LYD800pUC19c_LYD800 Phaseolus vulgaris 16049, 16320, 16177, 16320 579 901LYD801 pQFNc_LYD801 Phaseolus vulgaris 15987, 16241, 15999, 16241 580902 LYD802 TopoB_LYD802 Phaseolus vulgaris 16405, 16020 581 903 LYD803pQFNc_LYD803 Phaseolus vulgaris 16067, 16328, 16102, 16208 582 904LYD804 pMA-T_LYD804_GA 583 905 LYD806 pUC19c_LYD806 Phaseolus vulgaris16432, 16088, 16401, 15967 584 1123 LYD807 pQFNc_LYD807 Phaseolusvulgaris 16392, 15863, 16371, 15881 585 1124 LYD809 pQFNc_LYD809Phaseolus vulgaris 16077, 16332, 16161, 16235 586 908 LYD810pUC19_LYD810 Phaseolus vulgaris 16009, 16255 587 1125 LYD811pQFNc_LYD811 Phaseolus vulgaris 15997, 16350 588 1126 LYD812pUC19c_LYD812 Phaseolus vulgaris 15839, 16197, 15839, 16197 589 911LYD813 pQFNc_LYD813 Phaseolus vulgaris 15936, 16349, 15962, 16200 5901127 LYD814 pQFNc_LYD814 Phaseolus vulgaris 16010, 16226, 16010, 16226591 1128 LYD815 pUC19_LYD815 Phaseolus vulgaris 16059, 16326 592 914LYD816 pUC19c_LYD816 Phaseolus vulgaris 16008, 16224, 16159, 16256 5931129 LYD817 pQFNc_LYD817 Phaseolus vulgaris 15824, 16463, 15838, 16463594 916 LYD818 pQFNc_LYD818 Phaseolus vulgaris 16438, 16164, 16438,16164 595 1130 LYD819 pQFNc_LYD819 Phaseolus vulgaris 15951, 16338,16176, 16252 596 918 LYD821 pQFNc_LYD821 Phaseolus vulgaris 16031, 16346597 919 LYD823 pQFNc_LYD823 Phaseolus vulgaris 15944, 16485, 15944,16485 598 921 LYD824 pMA-T_LYD824_GA 599 922 LYD825 pQFNc_LYD825Phaseolus vulgaris 16033, 16479, 16033, 16479 600 923 LYD826pQFNc_LYD826 Phaseolus vulgaris 15952, 16278, 16104, 16278 601 924LYD828 pQFNc_LYD828 Phaseolus vulgaris 16094, 16284, 16094, 16284 6021131 LYD829 pUC19_LYD829 Phaseolus vulgaris 16146, 16302, 16146, 16245603 1132 LYD830 pQFNc_LYD830 Phaseolus vulgaris 16113, 16239, 16071,16221 604 928 LYD831 pUC19c_LYD831 CANOLA Brassica napus 15825, 15780,15825, 15772 605 929 LYD833 pQFNc_LYD833 CANOLA Brassica napus 16132,16339, 16064, 16307 606 930 LYD834 pQFNc_LYD834 CANOLA Brassica napus15937, 16183, 15937, 16183 607 1133 LYD835 pMA-T_LYD835_GA 608 932LYD836 pQFNc_LYD836 COTTON Gossypium hirsutum 16406, 15868, 16434, 15912609 933 LYD837 pQFNc_LYD837 COTTON Gossypium hirsutum 15965, 16271,15965, 16272 610 934 LYD838 pQFNc_LYD838 COTTON Gossypium hirsutum15931, 16194 611 935 LYD839 pQFNc_LYD839 COTTON Gossypium hirsutum16455, 15873, 16455, 15873 612 936 LYD840 pQFNc_LYD840 COTTON Gossypiumhirsutum 16397, 15896 613 937 LYD841 pQFNc_LYD841 COTTON Gossypiumhirsutum 15949, 16254, 16047, 16358 614 1134 LYD842 pQFNc_LYD842 COTTONGossypium hirsutum 16167, 16324, 15941, 16250 615 939 LYD843pQFNc_LYD843 COTTON Gossypium hirsutum 16389, 15877, 16389, 15877 616940 LYD844 pUC19c_LYD844 COTTON Gossypium hirsutum 16400, 15894, 16400,15894 617 1135 LYD845 pQFNc_LYD845 COTTON Gossypium hirsutum 16143,16182 618 1136 LYD846 pQFNc_LYD846 COTTON Gossypium hirsutum 16391,15902, 16378, 15893 619 1137 LYD847 pQFNc_LYD847 COTTON Gossypiumhirsutum 16030, 16343, 16030, 16343 620 1138 LYD848 pUC19_LYD848 COTTONGossypium hirsutum 16426, 16061 621 945 LYD849 pQFNc_LYD849 COTTONGossypium hirsutum 15842, 15888, 15856, 15889 622 1139 LYD850pQFNc_LYD850 COTTON Gossypium hirsutum 16000, 16291, 16000, 16291 6231140 LYD851 pMA- 624 948 RQ_LYD851_GA LYD852 pUC19c_LYD852 Medicago16415, 15910, 16447, 15886 625 1141 LYD853 pMA-T_LYD853_GA 626 950LYD854 pMA-T_LYD854_GA 627 951 LYD855 pMA_LYD855_GA 628 952 LYD856pUC19c_LYD856 Medicago 16417, 16475, 16417, 16475 629 1142 LYD857pMA-T_LYD857_GA 630 954 LYD858 pUC19c_LYD858 RICE Oryza sativa L. 16091,16262, 16091, 16262 631 955 LYD859 pQFNc_LYD859 RICE Oryza sativa L.15988, 16211 632 956 LYD860 pQFNc_LYD860 SOYBEAN Glycine max 16065,16222, 16014, 16243 633 957 LYD861 pUC19c_LYD861 SOYBEAN Glycine max16458, 16478, 16458, 16478 634 958 LYD863 pMA- 635 959 RQ_LYD863_GALYD864 pQFNc_LYD864 SOYBEAN Glycine max 16089, 16231 636 960 LYD865pQFNc_LYD865 SOYBEAN Glycine max 15957, 16331, 16044, 16216 637 1143LYD866 pMA- 638 962 RQ_LYD866_GA LYD867 pMA- 639 963 RQ_LYD867_GA LYD868pQFNc_LYD868 SOYBEAN Glycine max 15985, 16313, 15985, 16313 640 1144LYD869_H1 pMA- 696 1021 RQ_LYD869_H1_GA LYD870 pUC19_LYD870 SOYBEANGlycine max 15971, 16362, 16136, 16269 641 966 LYD871 pQFNc_LYD871SOYBEAN Glycine max 16066, 16323, 16066, 16329 642 967 LYD872pUC19c_LYD872 SOYBEAN Glycine max 16165, 16351, 16165, 16351 643 968LYD873 pQFNc_LYD873 SOYBEAN Glycine max 16112, 16368, 16022, 16270 644969 LYD874 pUC19_LYD874 SOYBEAN Glycine max 16138, 16340, 15979, 16315645 970 LYD876 pQFNc_LYD876 SOYBEAN Glycine max 16396, 16082, 16442,15968 646 971 LYD877 pQFNc_LYD877 SOYBEAN Glycine max 15964, 16333,16097, 16203 647 972 LYD878 pUC19_LYD878 SOYBEAN Glycine max 16416,15789, 16440, 15767 648 973 LYD879 pMA_LYD879_GA 649 974 LYD880pMA-T_LYD880_GA 650 975 LYD881 pQFNc_LYD881 SOYBEAN Glycine max 16007,16259, 15947, 16259 651 1145 LYD882 pQFNc_LYD882 SOYBEAN Glycine max16381, 15776, 16437, 15781 652 977 LYD883 pUC19_LYD883 SOYBEAN Glycinemax 16105, 16212, 16105, 16354 653 978 LYD884 pQFNc_LYD884 SOYBEANGlycine max 15989, 16214, 15976, 16369 654 979 LYD886 pQFNc_LYD886SOYBEAN Glycine max 16106, 16355, 16115, 16195 655 980 LYD887pUC19_LYD887 SOYBEAN Glycine max 16408, 15920, 16408, 15920 656 981LYD888 pMA- 657 982 RQ_LYD888_GA LYD890 pUC19_LYD890 SOYBEAN Glycine max15930, 16370 658 983 LYD891 pUC19_LYD891 SOYBEAN Glycine max 15833,15900, 15811, 15872 659 1146 LYD892 pMA-T_LYD892_GA 660 985 LYD893pQFNc_LYD893 TOMATO Lycopersicum ND 15878, 16285 661 986 LYD894pQFNc_LYD894 TOMATO Lycopersicum ND 15925, 16361, 15925, 16361 662 987LYD895 pQFNc_LYD895 TOMATO Lycopersicum ND 15948, 16283, 16149, 16265663 988 LYD896 pQFNc_LYD896 TOMATO Lycopersicum ND 15779, 15914, 15779,15915 664 989 LYD897 pUC19_LYD897 TOMATO Lycopersicum ND 16068, 16279,16129, 16279 665 990 LYD898 pQFNc_LYD898 TOMATO Lycopersicum ND 16380,15939, 16418, 16142 666 991 LYD899 pQFNc_LYD899 TOMATO Lycopersicum ND15938, 16301 667 1147 LYD900 pQFNc_LYD900 TOMATO Lycopersicum ND 15995,16267, 15995, 16263 668 1148 LYD901 pQFNc_LYD901 TOMATO Lycopersicum ND15959, 16213, 15959, 16213 669 994 LYD902 pQFNc_LYD902 TOMATOLycopersicum ND 16480, 16484, 16480, 16484 670 995 LYD903 TopoB_LYD903TOMATO Lycopersicum ND 16425, 15786, 16387, 15785 671 996 LYD904pUC19_LYD904 TOMATO Lycopersicum ND 16384, 15922, 16404, 15921 672 1149LYD905 pMA_LYD905_GA 673 998 LYD906 pUC19_LYD906 TOMATO Lycopersicum ND16457, 15901 674 999 LYD907 pQFNc_LYD907 TOMATO Lycopersicum ND 15943,15891, 15943, 15891 675 1000 LYD908 pQFNc_LYD908 TOMATO Lycopersicum ND16374, 15905, 16374, 15905 676 1150 LYD909 pUC19c_LYD909 TOMATOLycopersicum ND 16421, 15883, 16421, 15883 677 1002 LYD910pMA-T_LYD910_GA 678 1003 LYD911 pUC19_LYD911 TOMATO Lycopersicum ND15992, 16209, 16107, 16237 679 1151 LYD912 pMA-T_LYD912_GA 680 1005LYD913 pQFNc_LYD913 TOMATO Lycopersicum ND 16083, 16310 681 1006 LYD914pMA-T_LYD914_GA 682 1007 LYD915 pMA- 683 1008 RQ_LYD915_GA LYD917pMA-T_LYD917_GA 684 1009 LYD918 pQFNc_LYD918 TOMATO Lycopersicum ND16156, 16238, 16117, 16314 685 1010 LYD919 pQFNc_LYD919 TOMATOLycopersicum ND 16092, 16366, 16002, 16190 686 1011 LYD920 pQFNc_LYD920TOMATO Lycopersicum ND 16126, 16295, 16157, 16295 687 1012 LYD921TopoB_LYD921 TOMATO Lycopersicum ND 16413, 15765, 16453, 15774 688 1152LYD922 pMA-T_LYD922_GA 689 1014 LYD923 TopoB_LYD923 TOMATO LycopersicumND 15799, 15797, 15799, 15797 690 1153 LYD924 pUC19_LYD924 TOMATOLycopersicum ND 16428, 16144, 16395, 15975 691 1016 LYD925 pQFNc_LYD925TOMATO Lycopersicum ND 16116, 16330, 16012, 16277 692 1017 LYD926pMA-T_LYD926_GA 693 1018 LYD929 pQFNc_LYD929 Phaseolus vulgaris 15852,15879, 15843, 15876 694 1019 LYD930 pMA-T_LYD930_GA 695 1020 MGP1pUCsFN_MGP1 cotton 16074, 16359, 16169, 16360 704 1029 MGP14pMA-RQ_MGP14_GA 477 797 MGP2 pMA-T_MGP2_GA 705 1030 MGP4 pUCsFN_MGP4Soybean 16166, 15854, 16005, 15806 706 1031 MGP5 pMA-T_MGP5_GA 707 1032MGP7 pQFNc_MGP7 SORGHUM Sorghum bicolor 16080, 15870, 16080, 15870 7081034 MGP9 pMA-RQ_MGP9_GA 709 1035 Table 172: Provided are the genenames, cluster names, organisms from which they were derived, andpolynucleotide and polypeptide sequence identifiers of selected genes ofsome embodiments of the invention. “GA”—Gene Art (synthetically preparedgene sequence).

Example 23 Transforming Agrobacterium Tumefaciens Cells with BinaryVectors Harboring Putative Genes

Each of the binary vectors described in Example 22 above were used totransform Agrobacterium cells. Two additional binary constructs, havingonly the At6669 or the 35S promoter, or no additional promoter were usedas negative controls.

The binary vectors were introduced to Agrobacterium tumefaciens GV301 orLB4404 (for Arabidopsis) or AGL1 (for Brachypodium) competent cells(about 10⁹ cells/mL) by electroporation. The electroporation wasperformed using a MicroPulser electroporator (Biorad), 0.2 cm cuvettes(Biorad) and EC-2 electroporation program (Biorad). The treated cellswere cultured in LB liquid medium at 28° C. for 3 hours, then platedover LB agar supplemented with gentamycin (for Arabidopsis; 50 mg/L; forAgrobacterium strains GV301) or streptomycin (for Arabidopsis; 300 mg/L;for Agrobacterium strain LB4404); or with Carbenicillin (forBrachypodium; 50 mg/L) and kanamycin (for Arabidopsis and Brachypodium;50 mg/L) at 28° C. for 48 hours. Agrobacterium colonies, which weredeveloped on the selective media, were further analyzed by PCR using theprimers designed to span the inserted sequence in the pPI plasmid. Theresulting PCR products were isolated and sequenced to verify that thecorrect polynucleotide sequences of the invention are properlyintroduced to the Agrobacterium cells.

Example 24 Producing Transgenic Arabidopsis Plants Expressing SelectedGenes According to Some Embodiments of the Invention

Materials and Experimental Methods

Plant Transformation—

The Arabidopsis thaliana var Columbia (T₀ plants) were transformedaccording to the Floral Dip procedure [Clough S J, Bent A F. (1998)Floral dip: a simplified method for Agrobacterium-mediatedtransformation of Arabidopsis thaliana. Plant J. 16(6): 735-43; andDesfeux C, Clough S J, Bent A F. (2000) Female reproductive tissues werethe primary targets of Agrobacterium-mediated transformation by theArabidopsis floral-dip method. Plant Physiol. 123(3): 895-904] withminor modifications. Briefly, Arabidopsis thaliana Columbia (Col0) T₀plants were sown in 250 ml pots filled with wet peat-based growth mix.The pots were covered with aluminum foil and a plastic dome, kept at 4°C. for 3-4 days, then uncovered and incubated in a growth chamber at18-24° C. under 16/8 hours light/dark cycles. The T₀ plants were readyfor transformation six days before anthesis.

Single colonies of Agrobacterium carrying the binary vectors harboringthe yield genes were cultured in LB medium supplemented with kanamycin(50 mg/L) and gentamycin (50 mg/L). The cultures were incubated at 28°C. for 48 hours under vigorous shaking and centrifuged at 4000 rpm for 5minutes. The pellets comprising Agrobacterium cells were resuspended ina transformation medium which contained to half-strength (2.15 g/L)Murashige-Skoog (Duchefa); 0.044 μM benzylamino purine (Sigma); 112 μg/LB5 Gambourg vitamins (Sigma); 5% sucrose; and 0.2 ml/L Silwet L-77 (OSISpecialists, CT) in double-distilled water, at pH of 5.7.

Transformation of T₀ plants was performed by inverting each plant intoan Agrobacterium suspension such that the above ground plant tissue wassubmerged for 3-5 seconds. Each inoculated T₀ plant was immediatelyplaced in a plastic tray, then covered with clear plastic dome tomaintain humidity and was kept in the dark at room temperature for 18hours to facilitate infection and transformation. Transformed(transgenic) plants were then uncovered and transferred to a greenhousefor recovery and maturation. The transgenic T₀ plants were grown in thegreenhouse for 3-5 weeks until siliques were brown and dry, then seedswere harvested from plants and kept at room temperature until sowing.

For generating T₁ and T₂ transgenic plants harboring the genes, seedscollected from transgenic T₀ plants were surface-sterilized by soakingin 70% ethanol for 1 minute, followed by soaking in 5% sodiumhypochlorite and 0.05% triton for 5 minutes. The surface-sterilizedseeds were thoroughly washed in sterile distilled water then placed onculture plates containing half-strength Murashig-Skoog (Duchefa); 2%sucrose; 0.8% plant agar; 50 mM kanamycin; and 200 mM carbenicylin(Duchefa). The culture plates were incubated at 4° C. for 48 hours thentransferred to a growth room at 25° C. for an additional week ofincubation. Vital T₁ Arabidopsis plants were transferred to a freshculture plates for another week of incubation. Following incubation theT₁ plants were removed from culture plates and planted in growth mixcontained in 250 ml pots. The transgenic plants were allowed to grow ina greenhouse to maturity. Seeds harvested from T₁ plants were culturedand grown to maturity as T₂ plants under the same conditions as used forculturing and growing the T₁ plants.

Example 25 Transformation of Brachypodium Distachyon Plants with thePolynucleotides of the Invention

Similar to the Arabidopsis model plant, Brachypodium distachyon hasseveral features that recommend it as a model plant for functionalgenomic studies, especially in the grasses. Traits that make it an idealmodel include its small genome (˜160 Mbp for a diploid genome and 355Mbp for a polyploidy genome), small physical stature, a short lifecycle,and few growth requirements. Brachypodium is related to the major cerealgrain species but is understood to be more closely related to theTriticeae (wheat, barley) than to the other cereals. Brachypodium, withits polyploidy accessions, can serve as an ideal model for these grains(whose genomics size and complexity is a major barrier tobiotechnological improvement).

Brachypodium distachyon embryogenic calli are transformed using theprocedure described by Vogel and Hill (2008) [High-efficiencyAgrobacterium-mediated transformation of Brachypodium distachyon inbredline Bd21-3. Plant Cell Rep 27:471-478], Vain et al (2008)[Agrobacterium-mediated transformation of the temperate grassBrachypodium distachyon (genotypeBd21) for T-DNA insertionalmutagenesis. Plant Biotechnology J 6: 236-245], and Vogel J, et al.(2006) [Agrobacterium mediated transformation and inbred linedevelopment in the model grass Brachypodium distachyon. Plant Cell TissOrg. Cult. 85:199-211], each of which is fully incorporated herein byreference, with some minor modifications, which are briefly summarizedhereinbelow.

Callus initiation—Immature spikes (about 2 months after seeding) areharvested at the very beginning of seeds filling. Spikes are then huskedand surface sterilized with 3% NaClO containing 0.1% Tween 20, shaken ona gyratory shaker at low speed for 20 minutes. Following three rinseswith sterile distilled water, embryos are excised under a dissectingmicroscope in a laminar flow hood using fine forceps.

Excised embryos (size ˜0.3 mm, bell shaped) are placed on callusinduction medium (CIM) [LS salts (Linsmaier, E. M. & Skoog, F. 1965.Physiol. Plantarum 18, 100) and vitamins plus 3% sucrose, 6 mg/L CuSO₄,2.5 mg/l 2,4-Dichlorophenoxyacetic Acid, pH 5.8 and 0.25% phytagel(Sigma)] scutellar side down, 100 embryos on a plate, and incubated at28° C. in the dark. One week later, the embryonic calli is cleaned fromemerging roots, shoots and somatic calli, and was subcultured onto freshCIM medium. During culture, yellowish embryogenic callus (EC) appearedand are further selected (e.g., picked and transferred) for furtherincubation in the same conditions for additional 2 weeks. Twenty-fivepieces of sub-cultured calli are then separately placed on 90×15 mmpetri plates, and incubated as before for three additional weeks.

Transformation—As described in Vogel and Hill (2008, Supra),Agrobacterium is scraped off 2-day-old MGL plates (plates with the MGLmedium which contains: Tryptone 5 g/1, Yeast Extract 2.5 g/l, NaCl 5g/l, D-Mannitol 5 g/l, MgSO₄*7H₂O 0.204 g/l, K₂HPO₄ 0.25 g/l, GlutamicAcid 1.2 g/l, Plant Agar 7.5 g/1) and resuspended in liquid MS mediumsupplemented with 200 μM acetosyringone to an optic density (OD) at 600nm (OD₆₀₀) of 0.6. Once the desired OD was attained, 1 ml of 10%Synperonic PE/F68 (Sigma) per 100 ml of inoculation medium is added.

To begin inoculation, 300 callus pieces are placed in approximately 12plates (25 callus pieces in each plate) and covered with theAgrobacterium suspension (8-8.5 ml). The callus is incubated in theAgrobacterium suspension for 15 minutes with occasional gentle rocking.After incubation, the Agrobacterium suspension is aspirated off and thecalli are then transferred into co-cultivation plates, prepared byplacing a sterile 7-cm diameter filter paper in an empty 90×15 mm petriplate. The calli pieces are then gently distributed on the filter paper.One co-cultivation plate is used for two starting callus plates (50initial calli pieces). The co-cultivation plates are then sealed withparafilm and incubated at 22° C. in the dark for 3 days.

The callus pieces are then individually transferred onto CIM medium asdescribed above, which is further supplemented with 200 mg/l Ticarcillin(to kill the Agrobacterium) and Bialaphos (5 mg/L) (for selection of thetransformed resistant embryogenic calli sections), and incubated at 28°C. in the dark for 14 days.

The calli pieces are then transferred to shoot induction media (SIM; LSsalts and vitamins plus 3% Maltose monohydrate) supplemented with 200mg/l Ticarcillin, Bialaphos (5 mg/L), Indol-3-acetic acid (IAA) (0.25mg/L), and 6-Benzylaminopurine (BAP) (1 mg/L), and are sub-cultured inlight to the same media after 10 days (total of 20 days). At eachsub-culture all the pieces from a single callus are kept together tomaintain their independence and are incubated under the followingconditions: lighting to a level of 60 lE m-2 s-1, a 16-h light, 8-h darkphotoperiod and a constant 24° C. temperature. Plantlets emerged fromthe transformed calli.

When plantlets are large enough to handle without damage, they aretransferred to plates containing the above mentioned shoot inductionmedia (SIM) without Bialaphos. Each plantlet is considered as adifferent event. The plantlets grew axillary tillers and eventuallybecame bushy. Each bush from the same plant (event ID) is then dividedto tissue culture boxes (“Humus”) containing “rooting medium” [MS basalsalts, 3% sucrose, 3 g/L phytagel, 2 mg/l α-Naphthalene Acetic Acid(NAA) and 1 mg/L IAA and Ticarcillin 200 mg/L, PH 5.8). All plants in a“Humus box” are different plants of the same transformation event.

When plantlets establish roots they are transplanted to soil andtransferred to a greenhouse. To verify the transgenic status of plantscontaining the other constructs, T0 plants are subjected to PCR aspreviously described by Vogel et al. 2006 [Agrobacterium mediatedtransformation and inbred line development in the model grassBrachypodium distachyon. Plant Cell Tiss Org. Cult. 85:199-211].

Example 26 Evaluation of Transgenic Arabidopsis for Seed Yield and PlantGrowth Rate Under Normal Conditions in Greenhouse Assays (GH-SM Assays)

Assay 1: Seed Yield, Plant Biomass and Plant Growth Rate Under NormalGreenhouse Conditions—

This assay follows seed yield production, the biomass formation and therosette area growth of plants grown in the greenhouse at non-limitingnitrogen growth conditions. Transgenic Arabidopsis seeds were sown inagar media supplemented with ½ MS medium and a selection agent(Kanamycin). The T₂ transgenic seedlings were then transplanted to 1.7trays filled with peat and perlite in a 1:1 ratio. The plant were grownunder normal growth conditions which included irrigation of the trayswith a solution containing 6 mM inorganic nitrogen in the form of KNO₃with 1 mM KH₂PO₄, 1 mM MgSO₄, 2 mM CaCl₂ and microelements. Under normalconditions the plants grow in a controlled environment in a closedtransgenic greenhouse, temperature about 18-22° C., humidity around 70%.Irrigation was done by flooding with a water solution containing 6 mM N(nitrogen) (as described hereinabove), and flooding was repeatedwhenever water loss reached 50%. All plants were grown in the greenhouseuntil mature seeds. Seeds were harvested, extracted and weighted. Theremaining plant biomass (the above ground tissue) was also harvested,and weighted immediately or following drying in oven at 50° C. for 24hours.

Each construct was validated at its T₂ generation. Transgenic plantstransformed with a construct conformed by an empty vector carrying theAt6669 promoter (SEQ ID NO: 15751) and the selectable marker are used ascontrol.

The plants were analyzed for their overall size, growth rate, flowering,seed yield, 1,000-seed weight, dry matter and harvest index (HI-seedyield/dry matter). Transgenic plants performance was compared to controlplants grown in parallel under the same (e.g., identical) conditions.Mock-transgenic plants expressing the uidA reporter gene (GUS-Intron) orwith no gene at all, under the same promoter were used as controls.

The experiment was planned in nested randomized plot distribution. Foreach gene of the invention three to five independent transformationevents were analyzed from each construct.

Digital imaging—A laboratory image acquisition system, which consists ofa digital reflex camera (Canon EOS 300D) attached with a 55 mm focallength lens (Canon EF-S series), mounted on a reproduction device(Kaiser RS), which includes 4 light units (4×150 Watts light bulb) wasused for capturing images of plant samples.

The image capturing process was repeated every 2 days starting from day1 after transplanting till day 15. Same camera, placed in a custom madeiron mount, was used for capturing images of larger plants sawn in whitetubs in an environmental controlled greenhouse. The tubs were squareshape include 1.7 liter trays. During the capture process, the tubs wereplaced beneath the iron mount, while avoiding direct sun light andcasting of shadows.

An image analysis system was used, which consists of a personal desktopcomputer (Intel P4 3.0 GHz processor) and a public domain program—ImageJ1.39 [Java based image processing program which was developed at theU.S. National Institutes of Health and freely available on the internetat/rsbweb (dot) nih (dot) gov/]. Images are captured in resolution of 10Mega Pixels (3888×2592 pixels) and stored in a low compression JPEG(Joint Photographic Experts Group standard) format. Next, analyzed datawas saved to text files and processed using the JMP statistical analysissoftware (SAS institute).

Leaf analysis—Using the digital analysis leaves data was calculated,including leaf number, rosette area, rosette diameter, and leaf bladearea.

Vegetative growth rate: the relative growth rate (RGR) of leaf number[Formula VIII (described above)], rosette area (Formula IX above), plotcoverage (Formula XI above) and harvest index (Formula XV above) werecalculated with the indicated formulas.

Seeds average weight—At the end of the experiment all seeds werecollected. The seeds were scattered on a glass tray and a picture istaken. Using the digital analysis, the number of seeds in each samplewas calculated.

Dry weight and seed yield—On about day 80 from sowing, the plants wereharvested and left to dry at 30° C. in a drying chamber. The vegetativeportion above ground was separated from the seeds. The total weight ofthe vegetative portion above ground and the seed weight of each plotwere measured and divided by the number of plants.

Dry weight=total weight of the vegetative portion above ground(excluding roots) after drying at 30° C. in a drying chamber;

Seed yield per plant=total seed weight per plant (gr.)

1000 seed weight (the weight of 1000 seeds) (gr.).

Oil percentage in seeds—At the end of the experiment all seeds from eachplot were collected. Seeds from 3 plots were mixed grounded and thenmounted onto the extraction chamber. 210 ml of n-Hexane (Cat No. 080951Biolab Ltd.) were used as the solvent. The extraction was performed for30 hours at medium heat 50° C. Once the extraction has ended then-Hexane was evaporated using the evaporator at 35° C. and vacuumconditions. The process was repeated twice. The information gained fromthe Soxhlet extractor (Soxhlet, F. Die gewichtsanalytische Bestimmungdes Milchfettes, Polytechnisches J. (Dingier's) 1879, 232, 461) is usedto create a calibration curve for the Low Resonance NMR. The content ofoil of all seed samples was determined using the Low Resonance NMR(MARAN Ultra-Oxford Instrument) and its MultiQuant software package.

Silique length analysis—On day 50 from sowing, 30 siliques fromdifferent plants in each plot were sampled in block A. The chosensiliques were green-yellow in color and were collected from the bottomparts of a grown plant's stem. A digital photograph was taken todetermine silique's length.

Statistical analyses—To identify outperforming genes and constructs,results from the independent transformation events tested were analyzedseparately. Data was analyzed using Student's t-test and results wereconsidered significant if the p value was less than 0.1. The JMPstatistics software package was used (Version 5.2.1, SAS Institute Inc.,Cary, N.C., USA).

Tables 173-177 summarize the observed phenotypes of transgenic plantsexogenously expressing the gene constructs using the seed maturation(GH-SM) assays under normal conditions. The evaluation of each gene wasperformed by testing the performance of different number of events.Event with p-value<0.1 was considered statistically significant.

TABLE 173 Genes showing improved plant performance at Normal growthconditions under regulation of At6669 promoter Inflorescence Dry Weight[mg] Flowering Emergence Gene P- % P- % P- % Name Event # Ave. Val.Incr. Ave. Val. Incr. Ave. Val. Incr. LGP77 81452.2 — — — 24.0 0.04 −6 —— — CONT. — — — — 25.4 — — — — — LGP53 76966.2 1068.2 0.26  9 — — — — —— LGP53 76968.1 1135.9 0.20 16 — — — — — — LGP52 76962.1 1075.0 0.16 10— — — — — — LGP52 76963.1 — — — 20.8 0.19 −3 15.6 0.28 −3 LGP52 76963.3— — — 20.7 0.18 −3 14.6 L −9 CONT. —  976.9 — — 21.5 — — 16.0 — — LGP5876971.1 1042.1 0.19  7 — — — — — — LGP48 77202.1 1108.8 L 14 — — — — — —LGP48 77203.2 1061.6 0.15  9 — — — — — — LGP48 77204.6 1009.7 0.28  4 —— — — — — LGP47 76960.1 1081.2 L 11 — — — — — — LGP47 76960.2 1057.10.09  9 — — — — — — LGP47 76960.3 1013.4 0.28  5 — — — — — — CONT. — 969.7 — — — — — — — — LYD930 83831.3 1766.2 0.14 22 — — — — — — LYD93083832.3 1621.2 0.13 12 — — — — — — LYD930 83833.1 1588.8 0.05 10 — — — —— — LYD930 83834.3 1566.7 0.11  8 — — — — — — LYD881 84058.2 1517.5 0.28 5 — — — — — — LYD877 83630.3 1810.0 0.23 25 — — — — — — LYD877 83631.21598.8 0.04 10 — — — — — — LYD863 83808.4 1778.1 L 23 — — — — — — LYD86383810.6 1744.2 L 20 — — — — — — LYD863 83810.7 1630.0 0.09 12 — — — — —— LYD846 83531.3 1526.2 0.22  5 — — — — — — LYD846 83533.4 2084.4 L 44 —— — — — — LYD831 83805.1 1538.1 0.20  6 — — — — — — LYD788 83798.4 — — —21.2 0.03 −4 — — — LYD779 83704.1 1551.9 0.23  7 — — — — — — LYD77983704.2 1662.5 0.27 15 — — — — — — LYD776 83944.1 1635.8 0.23 13 — — — —— — LYD776 83947.6 1563.1 0.11  8 — — — — — — LYD764 83479.4 1845.0 L 27— — — — — — LYD764 83480.1 1701.9 L 17 — — — — — — LYD764 83483.1 1538.10.18  6 — — — — — — LYD764 83483.6 1609.4 0.07 11 — — — — — — LYD71584158.1 1735.6 0.28 20 21.3 0.04 −3 — — — LYD715 84158.3 — — — 21.5 0.22−2 — — — LYD710 83893.2 1704.9 L 18 — — — — — — LYD710 83895.3 1765.6 L22 21.2 0.18 −4 — — — LYD710 83895.6 1726.9 0.08 19 — — — — — — LYD71083896.4 1551.9 0.12  7 — — — — — — LYD708 83451.1 1572.4 0.07  8 — — — —— — LYD708 83451.2 1636.9 0.14 13 — — — — — — LYD708 83451.5 1611.7 0.0311 — — — — — — LYD700 84150.3 1870.0 L 29 — — — — — — LYD698 83778.11630.0 0.02 12 — — — — — — LYD698 83780.3 1558.1 0.23  7 — — — — — —CONT. — 1450.2 — — 22.0 — — — — — LGP77 81452.2 1327.4 0.18 14 20.7 0.18−3 — — — LGP77 81453.2 — — — 20.6 0.07 −4 — — — LGP77 81453.3 — — — 20.60.07 −4 — — — LGP77 81456.3 — — — 20.5 0.06 −4 — — — CONT. — 1160.8 — —21.4 — — — — — LGP73 81449.7 1240.8 0.07  6 — — — — — — LGP73 81449.81391.7 L 19 20.5 0.09 −4 — — — CONT. — 1169.1 — — 21.4 — — — — — LYD93083831.3 — — — 19.1 L −10  — — — LYD930 83832.3 1219.4 0.08  5 20.1 0.03−6 — — — LYD881 84058.5 — — — 20.3 0.20 −5 — — — LYD881 84058.6 1208.80.15  4 — — — — — — LYD881 84060.4 1221.9 0.16  5 — — — — — — LYD87783630.2 1256.2 0.01  8 — — — — — — LYD877 83630.3 1223.8 0.08  6 — — — —— — LYD863 83808.2 — — — 20.5 0.30 −4 — — — LYD863 83808.4 1251.9 0.02 8 — — — — — — LYD863 83810.6 1420.0 L 23 — — — — — — LYD863 83810.71326.9 0.08 14 — — — — — — LYD846 83531.3 1266.2 0.09  9 — — — — — —LYD846 83531.4 1255.6 0.04  8 — — — — — — LYD831 83803.1 1208.8 0.13  4— — — — — — LYD831 83803.3 — — — 20.0 0.02 −6 — — — LYD831 83803.5 — — —20.8 0.29 −3 — — — LYD831 83803.6 1236.9 0.16  7 — — — — — — LYD78883798.4 1360.6 L 17 — — — — — — LYD788 83800.1 1206.2 0.22  4 — — — — —— LYD788 83800.5 1207.5 0.16  4 — — — — — — LYD783 84170.3 1327.6 0.0415 — — — — — — LYD783 84172.2 1290.0 0.15 11 — — — — — — LYD779 83704.21286.9 0.28 11 20.2 0.04 −6 — — — LYD764 83479.4 1370.6 L 18 20.2 0.04−6 — — — LYD764 83480.1 1291.9 0.05 11 — — — — — — LYD764 83483.1 1194.40.29  3 — — — — — — LYD740 83461.2 1228.1 0.18  6 — — — — — — LYD74083462.1 1272.5 0.17 10 — — — — — — LYD715 84155.1 1223.8 0.06  6 — — — —— — LYD715 84155.5 — — — 20.3 0.05 −5 — — — LYD715 84156.5 1267.5 L  9 —— — — — — LYD715 84158.1 1298.8 0.21 12 — — — — — — LYD715 84158.31336.9 0.05 15 — — — — — — LYD713 83788.1 1247.5 0.02  8 — — — — — —LYD713 83788.3 1381.9 0.04 19 — — — — — — LYD713 83789.2 1201.9 0.18  4— — — — — — LYD713 83789.3 1211.4 0.11  5 — — — — — — LYD708 83451.11212.5 0.12  5 — — — — — — LYD708 83451.6 1283.2 0.04 11 — — — — — —LYD698 83778.1 1240.0 0.03  7 — — — — — — CONT. — 1159.1 — — 21.3 — — —— — LYD919 83642.2 1188.1 0.21  5 — — — — — — LYD919 83644.3 1259.4 0.0211 — — — — — — LYD913 84195.2 1213.7 0.13  7 — — — — — — LYD913 84195.41288.8 0.24 14 20.2 L −6 — — — LYD913 84198.4 1213.1 0.11  7 — — — — — —LYD913 84198.7 1181.9 0.27  5 — — — 13.9 0.24 −2 LYD909 84174.1 1212.40.26  7 — — — 13.9 0.24 −2 LYD909 84174.2 1251.6 0.03 11 — — — — — —LYD909 84174.4 — — — 20.4 0.02 −6 — — — LYD909 84177.1 — — — — — — 13.80.23 −3 LYD900  83738.10 1216.9 0.19  8 — — — — — — LYD900  83738.141198.1 0.15  6 20.5 0.04 −5 13.9 0.24 −2 LYD900 83738.8 1220.6 0.27  819.6 0.04 −9 — — — LYD898 83640.1 — — — 19.9 0.19 −8 — — — LYD89883641.5 1323.1 L 17 — — — — — — LYD898 83641.6 1200.0 0.14  6 20.4 0.02−6 — — — LYD898 83641.8 — — — 20.9 0.25 −3 — — — LYD896 83659.2 1488.30.03 32 20.0 L −7 — — — LYD896 83661.1 1190.0 0.24  5 — — — — — — LYD89683661.2 1219.4 0.26  8 — — — — — — LYD895 83537.4 — — — 20.4 0.11 −6 — —— LYD893 83952.5 — — — 20.2 L −6 — — — LYD893 83952.6 1183.8 0.24  521.1 0.19 −2 — — — LYD893 83952.7 — — — 19.9 L −8 13.9 0.24 −2 LYD88683636.1 1199.3 0.29  6 — — — — — — LYD882 84064.4 — — — 20.6 0.27 −5 — —— LYD882 84065.1 1322.1 L 17 — — — — — — LYD871 83715.4 1208.8 0.22  7 —— — — — — LYD871 83716.2 — — — 20.3 0.01 −6 13.9 0.24 −2 LYD848 84290.1— — — — — — 13.9 0.24 −2 LYD848 84290.3 1238.8 0.13 10 20.4 0.10 −6 — —— LYD840 84081.1 1194.4 0.25  6 21.2 0.30 −2 13.8 0.23 −3 LYD840 84085.21198.8 0.21  6 — — — 13.9 0.24 −2 LYD786 84582.1 1222.5 0.23  8 — — —13.8 0.23 −3 LYD786 84582.2 1255.0 0.03 11 — — — — — — LYD786 84584.4 —— — 20.6 0.18 −5 — — — LYD786 84585.4 1214.4 0.09  8 — — — — — — LYD74683898.2 — — — 20.1 L −7 — — — LYD746 83902.4 1208.1 0.25  7 20.4 0.25 −5— — — LYD745 84261.1 1236.9 0.08  9 — — — — — — LYD745 84262.1 1427.20.14 26 17.0 L −21  12.0 0.26 −15  LYD745 84263.1 — — — 20.4 0.02 −6 — —— LYD745 84264.2 — — — — — — 13.9 0.24 −2 LYD733 83766.2 1289.4 0.26 14— — — — — — LYD733 83768.1 1246.0 0.18 10 — — — — — — LYD717 84353.11200.0 0.26  6 — — — — — — LYD717 84356.1 1296.7 0.28 15 20.9 0.11 −3 —— — CONT. — 1129.6 — — 21.6 — — 14.2 — — LGP32 75394.2 — — — — — — 23.10.20 −2 LGP32 75397.4 — — — 29.0 0.15 −2 22.7 0.03 −4 CONT. — — — — 29.6— — 23.5 — — LGP74 81326.1 — — — 34.8 L −5 27.4 0.07 −4 LGP74 81328.1 —— — 35.5 L −3 27.3 0.03 −4 LGP74 81328.3 — — — — — — 27.0 L −5 CONT. — —— — 36.7 — — 28.6 — — LGP43 76955.1 — — — — — — 18.0 0.26 −1 LGP4376955.2 — — — 21.9 0.23 −2 18.0 0.26 −1 CONT. — — — — 22.4 — — 18.3 — —LGP71 82500.4 1447.5 0.13  9 — — — — — — LGP71 82502.4 1415.0 0.28  7 —— — — — — LGP71 82503.1 1568.3 0.12 18 24.0 0.21 −4 — — — CONT. — 1328.1— — 25.2 — — — — — LGP1 76250.4 — — — — — — 18.0 0.18 −0 CONT. — — — — —— — 18.1 — — LGP73 81449.8 1539.6 0.07 12 — — — — — — CONT. — 1375.8 — —— — — — — — LGP71 82503.1 — — — 24.0 0.03 −8 — — — CONT. — — — — 26.1 —— — — — LGP34 75739.3  909.4 0.17  4 — — — — — — CONT. —  878.3 — — — —— — — — LYD929 83647.2 — — — 22.0 0.06 −3 15.0 0.09 −1 LYD929 83649.1 —— — 19.6 L −13  15.0 0.09 −1 LYD929 83650.3 — — — 21.8 0.07 −4 — — —LYD922 83821.3 — — — — — — 14.9 0.07 −2 LYD922 83823.6 1263.1 0.12  521.8 0.05 −4 — — — LYD915 84657.1 — — — 22.0 0.08 −3 15.0 0.09 −1 LYD91584658.1 — — — 22.1 0.25 −2 — — — LYD913 84195.1 — — — 22.1 0.09 −3 15.00.09 −1 LYD913 84195.4 — — — 22.1 0.26 −2 — — — LYD909 84174.1 — — —21.9 0.18 −4 — — — LYD909 84174.4 — — — 21.2 0.02 −6 15.0 0.09 −1 LYD90984177.1 — — — 22.0 0.08 −3 — — — LYD909 84178.1 — — — 21.9 0.03 −4 15.00.09 −1 LYD899 83722.1 — — — — — — 15.0 0.09 −1 LYD899 83723.8 — — — — —— 15.0 0.09 −1 LYD895 83535.3 — — — 22.0 0.08 −3 — — — LYD895 83535.51288.8 0.08  7 — — — — — — LYD895 83537.3 — — — 22.2 0.14 −2 — — —LYD895 83537.4 — — — — — — 15.0 0.09 −1 LYD893 83950.1 — — — 22.0 0.06−3 15.0 0.09 −1 LYD893 83952.5 — — — 21.8 0.15 −4 — — — LYD893 83952.6 —— — 22.2 0.18 −2 15.0 0.09 −1 LYD848 84290.1 — — — — — — 15.0 0.09 −1LYD848 84290.3 — — — 22.2 0.18 −2 15.0 0.09 −1 LYD848 84292.1 — — — 22.10.09 −3 15.0 0.09 −1 LYD848 84292.5 1341.5 0.26 12 — — — 14.9 0.07 −2LYD840 84081.2 — — — 22.1 0.09 −3 — — — LYD840 84085.2 1426.9 0.20 1920.2 L −11  14.8 0.19 −3 LYD833 83511.1 — — — 21.6 0.03 −5 15.0 0.09 −1LYD833 83513.5 — — — — — — 14.8 0.19 −3 LYD821 84053.3 — — — 22.0 0.06−3 — — — LYD821 84054.2 — — — 22.1 0.10 −3 — — — LYD789 84131.3 1293.10.19  8 22.0 0.06 −3 — — — LYD789 84132.2 1331.2 L 11 — — — — — — LYD74683898.2 — — — — — — 15.0 0.09 −1 LYD733 83766.2 1290.6 0.05  7 — — — — —— LYD733 83768.1 — — — 22.1 0.11 −2 — — — LYD733 83768.4 — — — 21.9 0.14−3 15.0 0.09 −1 LYD717 84353.2 — — — — — — 15.0 0.09 −1 LYD717 84356.1 —— — 22.0 0.25 −3 — — — LYD717 84356.2 — — — — — — 15.0 0.09 −1 LYD70483781.1 — — — 22.2 0.21 −2 15.0 0.09 −1 LYD704 83785.1 — — — 22.1 0.11−2 — — — LYD704 83785.2 — — — — — — 15.0 0.09 −1 LYD704 83785.5 — — —21.8 0.05 −4 — — — CONT. — 1200.7 — — 22.7 — — 15.2 — — LGP54 77040.4 —— — — — — 16.4 0.01 −3 LGP53 76966.2 1166.4 0.01 16 — — — 16.1 0.08 −5LGP53 76968.1 1206.8 0.04 20 — — — — — — LGP52 76962.1 1128.6 0.27 12 —— — — — — LGP52 76963.1 1180.6 0.09 17 — — — 16.0 0.05 −5 LGP52 76963.3— — — 20.8 0.04 −5 15.6 L −8 LGP52 76965.2 1102.1 0.08 10 — — — 16.50.25 −3 CONT. — 1004.9 — — 21.9 — — 16.9 — — LYD919 83642.2 — — — 19.00.03 −3 12.0 0.13 −1 LYD919 83644.3 — — — — — — 12.0 0.13 −1 LYD900 83738.14 — — — 19.1 0.05 −3 — — — LYD900 83738.8 — — — 17.8 0.26 −9 — —— LYD898 83639.1 — — — — — — 12.0 0.13 −1 LYD898 83640.1 — — — 19.1 0.22−3 — — — LYD898 83641.5 1399.4 0.26  9 19.1 0.22 −3 12.0 0.13 −1 LYD89883641.8 — — — 18.8 0.03 −4 12.0 0.13 −1 LYD894 84360.1 — — — — — — 11.90.20 −2 LYD894 84361.1 — — — 18.8 0.03 −4 12.0 0.13 −1 LYD894 84362.1 —— — 18.4 0.14 −6 12.0 0.13 −1 LYD894 84362.2 — — — 19.2 0.15 −2 12.00.13 −1 LYD894 84362.3 — — — 18.8 0.24 −4 — — — LYD886 83634.3 — — — — —— 12.0 0.13 −1 LYD886 83635.4 — — — 18.8 0.08 −4 — — — LYD886 83636.1 —— — 18.5 0.23 −6 12.0 0.13 −1 LYD883 83911.2 1416.4 0.05 10 — — — — — —LYD883 83911.4 — — — 19.1 0.22 −3 — — — LYD883 83912.2 1382.1 0.15  718.6 0.16 −5 12.0 0.13 −1 LYD883 83912.3 — — — 19.1 0.06 −3 — — — LYD88284061.4 — — — 19.1 0.22 −3 12.0 0.13 −1 LYD882 84064.4 — — — 19.0 0.03−3 12.0 0.13 −1 LYD882 84065.1 — — — — — — 12.0 0.13 −1 LYD882 84065.3 —— — — — — 12.0 0.13 −1 LYD882 84065.7 — — — 19.3 0.16 −2 12.0 0.13 −1LYD871 83716.2 — — — 19.0 0.03 −3 12.0 0.13 −1 LYD871 83716.4 — — — 18.90.02 −4 12.0 0.13 −1 LYD871 83718.4 — — — 18.9 0.02 −4 — — — LYD87183718.6 — — — 19.0 0.05 −3 — — — LYD865 83729.1 — — — — — — 12.0 0.13 −1LYD865 83730.1 1643.0 0.26 27 — — — 12.0 0.13 −1 LYD865 83731.1 — — —18.6 0.04 −5 12.0 0.13 −1 LYD865 83733.5 — — — — — — 12.0 0.13 −1 LYD86583733.6 — — — 19.1 0.06 −3 — — — LYD839 83521.1 1376.2 0.20  7 18.8 0.03−4 12.0 0.13 −1 LYD839 83521.3 — — — 19.2 0.15 −2 12.0 0.13 −1 LYD83983522.1 1357.5 0.17  5 19.2 0.08 −2 — — — LYD811 83711.4 — — — — — —12.0 0.13 −1 LYD811 83713.3 — — — 19.3 0.18 −2 — — — LYD793 83499.71526.0 0.02 18 19.0 0.03 −3 — — — LYD793 83500.1 — — — — — — 12.0 0.13−1 LYD793 83500.4 — — — — — — 12.0 0.13 −1 LYD786 84582.1 — — — 19.30.21 −2 12.0 0.13 −1 LYD786 84584.4 — — — 19.3 0.18 −2 12.0 0.13 −1LYD786 84585.3 — — — 18.6 0.16 −5 — — — LYD786 84585.4 — — — 19.2 0.08−2 12.0 0.13 −1 LYD777 83489.3 1378.8 0.19  7 — — — 12.0 0.13 −1 LYD77783493.3 — — — — — — 12.0 0.13 −1 LYD772 84526.1 — — — — — — 11.9 0.17 −1LYD772 84529.2 1559.5 0.13 21 — — — 12.0 0.13 −1 LYD772 84529.3 — — — —— — 12.0 0.13 −1 LYD748 84918.1 — — — — — — 12.0 0.13 −1 LYD748 84918.3— — — 19.3 0.23 −1 12.0 0.13 −1 LYD748 84919.2 — — — 18.5 0.23 −6 12.00.13 −1 LYD748 84919.4 — — — 18.7 L −5 12.0 0.13 −1 LYD747 85011.1 — — —19.1 0.20 −3 12.0 0.13 −1 LYD747 85011.3 — — — 19.0 0.03 −3 12.0 0.13 −1LYD747 85011.5 — — — 19.1 0.05 −3 12.0 0.13 −1 LYD745 84261.4 — — — 18.90.02 −4 12.0 0.13 −1 LYD745 84262.1 1361.9 0.24  6 16.6 L −15  — — —LYD745 84263.1 — — — 17.9 0.25 −9 — — — LYD745 84264.2 — — — 18.9 0.02−4 12.0 0.13 −1 CONT. — 1289.0 — — 19.6 — — 12.1 — — LGP9 75517.2 — — —28.9 0.22 −3 22.6 0.26 −3 LGP10 75385.3 — — — — — — 22.5 0.23 −3 CONT. —— — — 29.6 — — 23.3 — — LGP45 77196.1  882.5 L 11 — — — — — — LGP1976938.3  874.7 0.05 10 — — — — — — CONT. —  796.8 — — — — — — — — LGP4776960.1 1091.2 0.05 18 — — — — — — CONT. —  927.0 — — — — — — — — Table173. “CONT.”—Control; “Ave.”—Average; “% Incr.” = % increment;“p-val.”—p-value, L- p < 0.01.

TABLE 174 Genes showing improved plant performance at Normal growthconditions under regulation of At6669 promoter Leaf Blade Area [cm²]Leaf Number Plot Coverage [cm²] Gene P- % P- % P- % Name Event # Ave.Val. Incr. Ave. Val. Incr. Ave. Val. Incr. LGP77 81452.2  0.949 0.03 15 9.54 0.25 4 56.2 0.06 18 LGP77 81456.3  0.887 0.15  7 — — — — — — CONT.—  0.826 — —  9.16 — — 47.8 — — LGP52 76963.1 — — — — — — 92.9 0.18 12LGP52 76965.2 — — — — — — 91.7 0.19 10 CONT. — — — — — — — 83.1 — —LGP48 77203.2 — — — 11.5 0.06 7 — — — LGP47 76956.1 — — — 11.2 0.26 4 —— — CONT. — — — — 10.8 — — — — — LYD930 83834.3 — — — 10.4 0.17 3 — — —LYD881 84058.5 1.97 0.29  8 — — — 106.1  0.23 10 LYD881 84060.4 — — —10.8 0.07 7 — — — LYD877 83630.1 — — — 10.8 0.30 6 — — — LYD877 83630.2— — — 10.8 0.16 6 — — — LYD877 83630.3 2.19 L 21 10.6 0.04 5 119.8  L 24LYD877 83630.4 — — — 11.2 0.05 11  112.5  0.13 16 LYD863 83808.1 — — —10.7 0.03 6 — — — LYD863 83810.7 — — — 10.8 0.16 6 — — — LYD846 83531.3— — — 10.5 0.15 4 — — — LYD846 83531.4 — — — — — — 104.1  0.29  8 LYD84683533.4 — — — 11.1 L 10  — — — LYD831 83803.1 1.97 0.20  8 — — — 104.5 0.25  8 LYD831 83803.3 2.00 0.12 10 10.9 L 8 107.2  0.15 11 LYD83183803.5 — — — — — — 104.7  0.26  8 LYD788 83798.4 — — — 10.9 L 8 119.0 0.12 23 LYD788 83800.4 — — — 10.4 0.24 3 — — — LYD788 83800.5 2.04 0.0712 — — — 109.0  0.10 13 LYD783 84170.3 2.05 0.05 13 — — — 110.1  0.08 14LYD779 83704.1 — — — 10.5 0.15 4 — — — LYD779 83704.2 1.94 0.27  6 10.70.03 6 108.4  0.10 12 LYD779 83708.2 — — — — — — 111.5  0.06 15 LYD77683944.1 — — — 10.7 0.11 6 — — — LYD776 83947.1 — — — — — — 106.0  0.25 9 LYD776 83947.4 — — — 10.5 0.15 4 — — — LYD764 83479.2 — — — 10.6 0.075 — — — LYD764 83479.4 2.10 0.13 15 10.9 0.04 8 120.8  0.06 25 LYD76483483.1 — — — 10.6 0.07 5 — — — LYD731 83454.2 — — — 10.8 0.01 7 — — —LYD731 83456.1 2.05 0.12 13 — — — 111.7  0.24 15 LYD715 84155.1 — — —10.6 0.07 5 — — — LYD715 84158.1 1.99 0.15  9 — — — — — — LYD715 84158.31.99 0.17  9 10.5 0.10 4 111.7  0.05 15 LYD713 83786.4 2.09 0.30 15 11.1L 9 114.1  0.17 18 LYD713 83788.3 2.06 0.08 13 10.9 0.11 8 120.0  L 24LYD713 83789.2 — — — 10.6 0.04 5 — — — LYD713 83789.3 — — — 10.8 0.02 6— — — LYD710 83893.2 — — — 10.4 0.24 3 — — — LYD710 83895.6 2.02 0.10 1111.0 L 9 115.5  0.03 19 LYD710 83896.1 2.03 0.24 12 10.6 0.07 5 112.3 0.21 16 LYD708 83451.7 2.06 0.23 13 — — — 112.8  0.21 17 LYD698 83780.42.00 0.13 10 — — — 112.2  0.04 16 CONT. — 1.82 — — 10.1 — — 96.8 — —LGP77 81452.2  0.762 0.02 14 — — — — — — LGP77 81453.3  0.711 0.11  6 —— — 39.5 0.16  6 CONT. —  0.668 — — — — — 37.1 — — LGP73 81449.7 1.090.22  7 — — — — — — LGP73 81449.8 1.20 0.01 17 10.5 0.04 8 69.3 L 24CONT. — 1.02 — —  9.72 — — 56.0 — — LYD930 83831.3 1.30 0.26 10 — — — —— — LYD930 83832.3 1.46 0.02 24 — — — 81.7 0.24 26 LYD930 83834.3 1.370.03 16 — — — 76.3 0.13 18 LYD881 84057.2 — — — 10.5 0.15 5 — — — LYD87783630.4 — — — 11.2 0.01 12  — — — LYD877 83631.2 — — — 11.1 0.20 12  — —— LYD863 83810.7 1.33 0.15 13 10.9 0.10 10  76.2 0.05 17 LYD846 83531.3— — — — — — 70.5 0.29  9 LYD831 83803.3 1.35 0.14 14 — — — 75.0 0.07 15LYD788 83800.4 1.45 L 23 — — — 81.4 0.01 25 LYD783 84170.1 — — — 10.60.28 7 74.5 0.22 15 LYD783 84170.3 — — — — — — 71.6 0.24 10 LYD77983704.2 — — — 10.9 0.02 9 74.9 0.07 15 LYD779 83708.2 1.29 0.17 10 — — —72.5 0.18 12 LYD764 83479.4 — — — 10.7 0.06 7 72.3 0.15 11 LYD76483483.1 1.34 0.06 14 11.0 0.02 10  78.6 0.03 21 LYD740 83462.1 1.26 0.29 7 — — — 70.6 0.26  9 LYD715 84155.5 — — — 11.2 0.01 12  85.6 0.10 32LYD715 84158.1 — — — — — — 83.5 0.29 29 LYD715 84158.3 — — — — — — 72.10.16 11 LYD713 83786.4 — — — 10.6 0.07 7 — — — LYD713 83788.3 — — — — —— 72.3 0.15 11 LYD713 83789.3 — — — 10.4 0.18 5 71.5 0.25 10 CONT. —1.18 — —  9.96 — — 64.9 — — LGP49 77652.6 — — — 11.3 0.17 4 113.4  0.1713 CONT. — — — — 10.8 — — 100.2  — — LYD919 83642.2 1.49 0.03 19 11.10.02 11  91.4 0.09 33 LYD919 83644.3 — — — 10.8 0.25 8 74.8 0.22  9LYD919 83645.1 — — — 10.6 0.02 6 78.3 0.07 14 LYD913 84195.2 — — — 10.60.03 6 75.9 0.27 11 LYD913 84198.4 1.40 0.10 12 10.4 0.15 4 77.1 0.08 12LYD913 84198.7 — — — — — — 85.0 0.24 24 LYD909 84174.2 1.54 0.08 23 10.8L 8 90.1 0.15 31 LYD909 84174.4 1.57 L 25 10.9 0.03 9 92.4 L 35 LYD90984177.1 1.39 0.13 11 10.5 0.03 5 81.3 0.02 19 LYD909 84178.3 1.38 0.1510 — — — 79.6 0.03 16 LYD900  83738.10 1.49 0.06 18 11.1 0.29 11  88.20.06 29 LYD900  83738.14 1.48 0.08 18 — — — 85.2 0.09 24 LYD900 83738.81.64 0.25 31 10.9 0.21 9 99.0 0.18 44 LYD898 83639.1 — — — 10.8 0.28 8 —— — LYD898 83640.1 1.53 0.22 22 — — — 90.6 0.22 32 LYD898 83641.6 1.380.15 10 10.6 0.17 6 81.6 0.02 19 LYD896 83659.5 — — — — — — 76.7 0.16 12LYD896 83661.1 — — — 10.8 0.25 8 — — — LYD896 83661.2 1.39 0.15 11 — — —80.0 0.10 17 LYD896 83661.4 1.37 0.22  9 10.9 L 9 80.8 0.02 18 LYD89583535.4 1.42 0.12 13 10.8 L 8 84.1 0.10 23 LYD895 83537.3 — — — 10.40.15 4 — — — LYD895 83537.4 — — — 10.4 0.15 4 — — — LYD893 83951.1 1.480.04 18 10.8 L 8 88.7 L 29 LYD893 83952.5 1.47 0.03 17 10.6 0.11 6 86.30.02 26 LYD893 83952.6 — — — 10.8 L 8 85.5 0.25 25 LYD893 83952.7 — — —10.8 L 8 84.0 0.14 23 LYD886 83635.4 1.45 0.06 15 10.4 0.06 4 84.2 0.0323 LYD886 83636.1 — — — — — — 81.7 0.19 19 LYD882 84061.1 1.53 0.01 2210.9 0.09 9 90.3 0.04 32 LYD882 84064.4 1.40 0.12 12 — — — 82.0 0.10 20LYD882 84065.1 — — — 10.4 0.15 4 — — — LYD882 84065.7 1.42 0.26 13 11.00.07 10  83.0 0.08 21 LYD871 83715.4 1.35 0.24  8 10.6 0.28 6 77.3 0.0713 LYD871 83716.2 1.37 0.21  9 — — — 77.7 0.07 13 LYD871 83718.6 1.360.21  9 10.6 0.17 6 78.3 0.07 14 LYD848 84290.3 1.53 0.07 22 11.1 0.2411  92.8 L 35 LYD848 84290.4 — — — — — — 88.4 0.29 29 LYD848 84292.51.36 0.27  8 10.8 L 8 85.6 L 25 LYD840 84085.2 — — — 10.4 0.18 4 76.50.19 12 LYD840 84085.4 — — — — — — 75.7 0.13 10 LYD786 84582.2 — — — — —— 75.4 0.17 10 LYD786 84584.4 — — — — — — 76.5 0.15 12 LYD786 84585.41.41 0.10 12 10.4 0.18 4 80.3 0.04 17 LYD746 83898.2 1.46 0.04 16 10.9 L9 84.8 L 24 LYD746 83902.2 1.54 0.22 23 11.1 0.02 11  90.9 0.14 33LYD746 83902.4 1.41 0.15 12 10.5 0.07 5 83.0 0.01 21 LYD745 84261.1 — —— 10.9 L 9 81.1 0.16 18 LYD745 84261.4 1.53 0.01 22 10.6 0.03 6 88.4 L29 LYD745 84262.1 1.69 L 35 11.2 L 12  104.6  L 53 LYD745 84264.2 1.410.19 13 10.5 0.07 5 82.9 0.01 21 LYD733 83766.2 — — — — — — 75.7 0.14 10LYD733 83768.3 1.48 0.03 18 10.8 0.12 8 89.3 L 30 LYD717 84353.1 — — — —— — 78.0 0.09 14 LYD717 84354.2 — — — — — — 76.4 0.10 11 LYD717 84356.21.51 0.02 20 11.1 L 11  92.9 L 35 CONT. — 1.25 — — 10.0 — — 68.6 — —LGP6 75670.2 1.20 0.23  6 — — — — — — LGP32 75397.4 1.29 0.10 14 11.10.06 9 81.3 0.08 20 LGP12 78567.3 1.25 0.09 10 — — — — — — CONT. — 1.13— — 10.1 — — 67.5 — — LGP74 81325.1 — — — 11.9 0.29 7 — — — LGP7481328.3 1.59 0.06 15 — — — 94.1 0.06 18 CONT. — 1.38 — — 11.1 — — 79.7 —— LGP74 81325.1 1.29 0.18  6 — — — 77.2 0.20  8 LGP74 81328.3 1.37 0.1713 11.0 0.24 6 84.8 0.15 19 CONT. — 1.22 — — 10.4 — — 71.3 — — LGP7182503.1 1.16 0.08 29  9.83 0.02 8 68.2 0.06 38 CONT. —  0.902 — —  9.12— — 49.5 — — LYD911 86502.3 — — — 10.7 0.15 3 — — — LYD911 86503.1 — — —11.3 0.03 9 101.8  0.04 21 LYD907 84976.1 1.71 0.10 12 10.6 0.21 3 95.70.10 14 LYD907 84979.1 1.64 0.30  7 — — — — — — LYD907 84979.2 — — —11.1 0.06 7 — — — LYD904 84497.2 — — — — — — 94.3 0.11 12 LYD904 84499.22.00 L 31 10.6 0.21 3 111.8  L 33 LYD902 84948.5 — — — — — — 105.2  0.2825 LYD899 83722.1 — — — 10.8 0.14 4 — — — LYD899 83723.8 — — — 11.3 0.239 — — — LYD896 83661.4 — — — 11.1 L 8 — — — LYD867 85536.2 — — — 11.10.06 7 — — — LYD867 85536.5 — — — — — — 91.1 0.24  8 LYD844 85192.1 — —— — — — 93.9 0.16 12 LYD844 85192.3 1.84 0.29 20 — — — — — — LYD84485192.4 1.65 0.23  8 — — — — — — LYD844 85192.7 1.79 0.06 17 — — — 99.60.03 18 LYD844 85192.8 — — — 10.8 0.06 5 — — — LYD825 85881.2 — — — 10.80.14 4 — — — LYD825 85883.1 1.82 0.02 19 — — — 100.3  0.02 19 LYD82585884.2 1.83 0.02 20 — — — 99.1 0.03 18 LYD812 85560.1 1.65 0.27  8 — —— 91.6 0.25  9 LYD812 85560.2 2.05 L 34 — — — 107.5  L 28 LYD812 85564.1— — — 10.6 0.28 3 94.5 0.30 12 LYD778 85053.2 — — — 11.4 L 10  — — —LYD778 85053.3 — — — 10.9 0.25 6 91.9 0.21  9 LYD778 85053.4 — — — — — —103.2  0.14 23 LYD772 84526.1 1.87 0.28 22 — — — 102.0  0.29 21 LYD73084258.1 — — — 11.1 0.06 7 — — — LYD711 85316.3 2.02 0.24 32 — — — 107.1 0.25 27 LYD711 85316.5 — — — 10.9 0.07 5 108.4  0.21 29 CONT. — 1.53 — —10.3 — — 84.1 — — LGP1 76249.3 — — — 11.4 0.16 4 — — — CONT. — — — —11.0 — — — — — LGP71 82503.1 — — —  9.58 0.15 4 49.2 0.13 10 CONT. — — ——  9.25 — — 44.5 — — LYD929 83647.2 — — — 11.1 0.23 3 — — — LYD92983649.1 1.81 0.18 11 — — — — — — LYD929 83651.2 — — — 11.4 0.17 6 106.2 0.14 12 LYD922 83823.6 1.83 0.06 12 11.4 0.22 6 106.4  0.13 12 LYD91584657.1 1.98 0.27 22 — — — 114.8  0.27 21 LYD913 84195.1 2.00 0.13 23 —— — 114.0  0.03 20 LYD909 84174.1 1.81 0.11 11 11.3 0.04 5 109.4  0.1915 LYD909 84174.4 — — — 11.6 0.17 7 — — — LYD909 84178.1 — — — 11.2 0.104 — — — LYD893 83950.1 1.79 0.13 10 — — — 107.7  0.21 13 LYD893 83952.5— — — 11.9 0.05 10  107.4  0.11 13 LYD893 83952.6 — — — 11.4 0.02 6 — —— LYD848 84289.1 1.92 0.02 18 12.1 0.07 12  121.3  0.06 28 LYD84884292.1 — — — 11.2 0.10 4 — — — LYD848 84292.5 — — — 11.2 0.10 4 — — —LYD840 84081.2 — — — 11.4 0.02 6 107.6  0.30 13 LYD840 84085.2 1.89 0.0616 12.1 L 13  114.1  0.03 20 LYD833 83511.4 — — — 11.6 0.05 7 — — —LYD833 83512.2 — — — 11.4 0.05 6 — — — LYD833 83513.5 1.92 0.02 18 11.50.02 7 124.4  L 31 LYD821 84054.2 1.74 0.23  7 — — — 103.0  0.26  9LYD789 84132.3 — — — 11.3 0.04 5 102.7  0.28  8 LYD733 83768.1 — — —11.2 0.10 4 — — — LYD717 84354.2 — — — 11.3 0.13 5 — — — LYD717 84356.2— — — 11.2 0.06 4 — — — LYD704 83785.2 1.74 0.25  7 — — — — — — LYD70483785.5 — — — 11.2 0.10 4 — — — CONT. — 1.63 — — 10.8 — — 94.9 — — LGP5276963.1 1.77 0.21 13 — — — 104.0  0.28 12 CONT. — 1.57 — — — — — 92.8 —— LYD919 83642.2 1.57 0.06 10 11.6 0.26 9 95.9 L 17 LYD919 83644.3 — — —— — — 89.5 0.28  9 LYD919 83646.1 1.56 0.16 10 11.2 0.06 5 91.1 0.20 11LYD900  83738.10 — — — 10.9 0.26 3 — — — LYD900  83738.11 — — — 11.30.08 6 — — — LYD900  83738.14 — — — 11.2 0.13 5 — — — LYD900 83738.8 — —— 11.1 0.08 5 — — — LYD898 83641.5 1.53 0.27  8 — — — 90.0 0.24 10LYD898 83641.8 — — — — — — 93.2 0.14 14 LYD894 84361.1 1.53 0.21  8 — —— — — — LYD894 84362.1 — — — 11.1 0.23 4 — — — LYD894 84362.2 1.52 0.08 7 — — — 87.3 0.11  7 LYD886 83634.2 — — — — — — 87.0 0.17  6 LYD88683634.3 — — — — — — 87.6 0.26  7 LYD886 83636.1 1.58 0.02 11 — — — 93.1L 14 LYD883 83911.4 1.49 0.24  5 — — — — — — LYD883 83912.2 1.50 0.16  5— — — — — — LYD883 83912.3 1.75 L 23 11.0 0.22 3 101.4  L 24 LYD88284065.1 1.51 0.16  6 — — — 90.4 0.06 10 LYD871 83716.2 — — — 11.5 0.02 895.8 0.03 17 LYD871 83718.6 1.64 0.06 15 11.2 0.06 6 99.8 0.09 22 LYD86583731.1 1.70 L 20 — — — 103.1  0.10 26 LYD865 83733.5 1.52 0.03  7 11.10.11 5 88.0 0.09  8 LYD839 83521.1 — — — 11.3 0.03 6 — — — LYD83983522.1 — — — — — — 85.2 0.30  4 LYD811 83711.4 1.52 0.27  7 11.1 0.25 588.2 0.29  8 LYD811 83713.3 1.64 0.06 16 11.1 0.13 4 95.9 0.11 17 LYD79383499.2 1.61 0.12 13 — — — 91.6 0.02 12 LYD793 83499.7 — — — — — — 88.80.07  8 LYD777 83489.3 1.59 L 12 11.7 L 10  96.5 L 18 LYD777 83492.3 — —— 11.2 0.13 5 — — — LYD777 83493.3 — — — — — — 85.6 0.25  5 LYD77284526.1 1.48 0.20  4 — — — 86.7 0.14  6 LYD772 84529.2 1.57 0.21 10 11.30.03 6 92.0 0.21 12 LYD772 84529.3 — — — 11.0 0.22 3 — — — LYD74884919.1 — — — 11.2 0.13 5 — — — LYD748 84919.4 1.49 0.29  5 — — — — — —LYD747 85011.3 — — — — — — 85.6 0.25  5 LYD747 85012.1 — — — 11.0 0.22 3— — — LYD745 84261.1 1.56 0.09 10 11.2 0.06 6 89.5 0.12  9 LYD74584262.1 1.62 L 14 — — — 93.4 0.21 14 LYD745 84263.1 1.58 L 12 — — — 93.50.05 14 CONT. — 1.42 — — 10.6 — — 81.9 — — LGP9 75515.1 — — — 10.2 0.095 — — — LGP44 75765.3 — — — 10.5 0.03 8 — — — LGP10 75385.3 — — — 10.50.07 8 — — — CONT. — — — —  9.67 — — — — — LGP46 77258.3 — — —  9.750.11 3 — — — CONT. — — — —  9.44 — — — — — Table 174. “CONT.”—Control;“Ave.”—Average; “% Incr.” = % increment; “p-val.”—p-value, L- p < 0.01.

TABLE 175 Genes showing improved plant performance at Normal growthconditions under regulation of At6669 promoter RGR Of Leaf RGR Of PlotRGR Of Rosette Number Coverage Diameter Gene P- % P- % P- % Name Event #Ave. Val. Incr. Ave. Val. Incr. Ave. Val. Incr. LGP77 81452.2 — — — 7.16 0.07 17 — — — CONT. — — — —  6.10 — — — — — LGP52 76963.1 — — —12.6 0.23 10 — — — LGP52 76965.2 — — — 12.4 0.30  8 — — — CONT. — — — —11.4 — — — — — LGP48 77202.4 0.749 0.11 15 — — — 0.511 0.14  6 LGP4877203.2 0.779 L 20 — — — — — — LGP47 76956.1 0.760 0.02 17 — — — — — —LGP47 76960.2 0.734 0.15 13 — — — — — — CONT. — 0.651 — — — — — 0.484 —— LYD877 83630.1 — — — — — — 0.571 0.23 14 LYD877 83630.3 — — — 15.30.12 25 0.615 0.05 23 LYD877 83630.4 0.707 0.09 20 14.4 0.26 17 0.5690.25 14 LYD863 83808.1 0.689 0.18 16 — — — — — — LYD863 83810.6 0.6830.20 16 — — — — — — LYD863 83810.7 — — — — — — 0.577 0.20 15 LYD84683531.3 0.673 0.22 14 — — — — — — LYD846 83533.4 0.735 0.06 24 — — — — —— LYD831 83803.3 0.709 0.10 20 — — — — — — LYD831 83803.6 — — — — — —0.565 0.29 13 LYD788 83798.4 — — — 15.0 0.16 22 0.583 0.16 17 LYD78883800.5 — — — — — — 0.570 0.23 14 LYD779 83708.2 — — — — — — 0.577 0.1915 LYD776 83944.1 0.775 0.01 31 — — — — — — LYD776 83947.1 — — — — — —0.564 0.27 13 LYD776 83947.2 0.668 0.26 13 — — — — — — LYD764 83479.20.669 0.27 13 — — — — — — LYD764 83479.4 0.676 0.25 14 15.3 0.13 240.590 0.12 18 LYD731 83454.2 0.668 0.29 13 — — — — — — LYD731 83456.1 —— — — — — 0.570 0.25 14 LYD731 83458.1 — — — — — — 0.562 0.28 12 LYD71383786.4 0.683 0.22 16 14.5 0.25 18 — — — LYD713 83788.1 0.699 0.20 18 —— — — — — LYD713 83788.3 — — — 15.5 0.09 26 0.576 0.19 15 LYD713 83789.30.724 0.06 22 — — — — — — LYD710 83893.2 0.683 0.17 16 — — — — — —LYD710 83895.6 — — — 14.5 0.25 18 — — — LYD710 83896.1 — — — 14.4 0.2817 — — — LYD708 83451.7 — — — 14.4 0.27 17 0.581 0.18 16 LYD700 84151.10.691 0.20 17 — — — — — — LYD700 84151.4 0.694 0.14 17 — — — — — —LYD698 83780.3 0.679 0.26 15 — — — — — — LYD698 83780.4 — — — 14.4 0.2717 0.563 0.27 13 CONT. — 0.591 — — 12.3 — — 0.501 — — LGP77 81452.2 — —— — — — 0.435 0.14 10 CONT. — — — — — — — 0.395 — — LGP73 81449.3 — — —— — — 0.399 0.07  8 LGP73 81449.7 — — — — — — 0.402 L  9 LGP73 81449.80.624 0.11 24  8.37 L 24 0.400 0.02  9 CONT. — 0.505 — —  6.77 — — 0.368— — LYD930 83832.3 — — — 10.7 0.12 27 0.480 0.14 16 LYD930 83834.3 — — —10.0 0.25 19 — — — LYD877 83631.2 0.820 0.19 24 — — — — — — LYD86383810.7 — — —  9.88 0.30 17 — — — LYD788 83800.4 — — — 10.7 0.10 270.486 0.09 17 LYD764 83483.1 — — — 10.3 0.19 22 — — — LYD715 84155.50.791 0.28 20 11.2 0.06 32 0.487 0.10 18 LYD715 84158.1 — — — 10.9 0.1029 0.463 0.29 12 LYD713 83786.4 0.778 0.30 18 — — — — — — LYD713 83789.2— — — 10.5 0.16 24 0.477 0.17 15 CONT. — 0.659 — —  8.44 — — 0.414 — —LGP49 77652.6 — — — 13.9 0.18 13 — — — CONT. — — — — 12.3 — — — — —LYD919 83642.2 0.810 0.13 25 12.1 0.04 35 0.539 0.03 24 LYD913 84198.7 —— — 11.1 0.16 23 — — — LYD909 84174.2 — — — 11.8 0.06 31 0.492 0.20 14LYD909 84174.4 — — — 12.2 0.03 36 0.490 0.20 13 LYD909 84177.1 — — —10.7 0.24 19 0.480 0.30 11 LYD909 84178.3 — — — 10.5 0.30 17 — — —LYD900  83738.10 0.786 0.20 21 11.6 0.08 29 0.489 0.23 13 LYD900 83738.14 — — — 11.2 0.13 25 0.503 0.13 16 LYD900 83738.8 — — — 12.90.02 44 0.536 0.04 24 LYD898 83639.1 — — — 10.5 0.28 17 — — — LYD89883640.1 — — — 11.9 0.06 32 0.498 0.18 15 LYD898 83641.6 — — — 10.7 0.2319 — — — LYD896 83659.2 0.775 0.25 19 — — — — — — LYD896 83659.5 — — — —— — 0.484 0.26 12 LYD896 83661.2 — — — 10.5 0.29 17 — — — LYD896 83661.40.777 0.23 20 10.7 0.24 19 0.494 0.19 14 LYD895 83535.4 — — — 11.0 0.1722 — — — LYD893 83951.1 — — — 11.7 0.07 30 — — — LYD893 83952.5 — — —11.4 0.10 27 0.520 0.06 20 LYD893 83952.6 — — — 11.3 0.14 25 — — —LYD893 83952.7 — — — 11.0 0.17 22 0.496 0.17 14 LYD886 83634.2 — — —10.6 0.28 18 0.490 0.24 13 LYD886 83635.4 — — — 11.1 0.16 23 0.504 0.1316 LYD886 83636.1 — — — 10.8 0.22 20 — — — LYD882 84061.1 — — — 11.90.05 32 0.507 0.11 17 LYD882 84064.4 — — — 10.7 0.24 19 — — — LYD88284065.7 0.785 0.19 21 10.9 0.20 21 — — — LYD871 83716.2 — — — — — —0.490 0.22 13 LYD848 84290.3 — — — 12.2 0.03 35 0.488 0.23 13 LYD84884290.4 0.946 0.01 45 11.6 0.09 29 — — — LYD848 84292.5 — — — 11.2 0.1325 0.491 0.21 13 LYD786 84582.1 — — — 11.0 0.18 23 0.484 0.28 12 LYD78684585.4 — — — 10.5 0.29 17 — — — LYD746 83898.2 0.760 0.27 17 11.1 0.1424 — — — LYD746 83902.2 0.759 0.28 17 12.0 0.06 33 0.493 0.21 14 LYD74683902.4 — — — 10.9 0.18 21 0.487 0.23 12 LYD745 84261.1 0.780 0.23 2010.6 0.27 17 — — — LYD745 84261.4 — — — 11.6 0.08 29 0.509 0.09 17LYD745 84262.1 0.771 0.25 19 13.8 L 54 0.541 0.02 25 LYD745 84264.2 — —— 10.8 0.20 21 0.491 0.21 13 LYD733 83768.3 — — — 11.8 0.06 31 0.4960.17 15 LYD717 84353.1 0.769 0.28 18 — — — — — — LYD717 84356.2 — — —12.2 0.03 36 0.497 0.15 15 CONT. — 0.650 — —  9.00 — — 0.433 — — LGP4677256.1 0.906 0.04 30 — — — — — — LGP46 77258.3 0.781 0.08 12 — — — — —— LGP46 77259.6 0.805 0.17 15 — — — — — — LGP46 77260.2 0.750 0.29  7 —— — — — — LGP45 77196.1 — — — — — — 0.544 0.26  4 LGP45 77196.5 0.7890.20 13 — — — — — — LGP19 76938.3 0.805 0.21 15 — — — — — — LGP1976939.2 0.773 0.10 11 — — — — — — LGP19 76940.1 0.820 0.17 18 — — — — —— CONT. — 0.698 — — — — — 0.520 — — LGP6 75670.2 — — — — — — 0.466 0.21 5 LGP32 75397.4 — — — 10.5 0.08 22 0.517 0.03 17 LGP12 78567.3 — — — —— — 0.488 0.08 10 CONT. — — — —  8.60 — — 0.443 — — LGP74 81325.1 0.7450.28 10 — — — — — — LGP74 81328.3 — — — 11.3 0.05 19 0.451 0.09  9 CONT.— 0.680 — —  9.43 — — 0.413 — — LGP43 76953.2 0.680 0.17 22 — — — — — —LGP43 76953.5 0.666 0.14 20 — — — — — — CONT. — 0.557 — — — — — — — —LGP74 81325.1 — — —  9.83 0.18  9 0.481 0.20  5 LGP74 81328.3 — — — 10.80.16 20 0.505 0.12 10 CONT. — — — —  9.04 — — 0.460 — — LGP71 82503.10.613 0.13  8  8.80 0.08 38 0.477 0.22 19 CONT. — 0.568 — —  6.37 — —0.400 — — LYD911 86503.1 — — — 13.0 0.22 21 — — — LYD904 84498.5 — — —13.2 0.22 24 — — — LYD904 84499.2 — — — 14.5 0.05 35 0.576 0.06 20LYD902 84948.5 — — — 13.3 0.16 25 0.551 0.18 14 LYD899 83723.8 0.7860.26 16 — — — — — — LYD867 85535.2 — — — 13.6 0.17 27 0.547 0.23 13LYD867 85536.5 — — — — — — 0.538 0.24 12 LYD844 85192.3 — — — 13.2 0.2023 0.550 0.18 14 LYD844 85192.7 — — — 12.7 0.28 19 — — — LYD844 85192.8— — — 13.5 0.17 26 — — — LYD825 85882.4 — — — — — — 0.554 0.19 15 LYD82585883.1 — — — 13.0 0.22 21 0.544 0.21 13 LYD825 85884.2 — — — 12.7 0.2918 — — — LYD812 85560.2 — — — 13.8 0.10 29 0.575 0.07 19 LYD812 85564.1— — — — — — 0.539 0.27 12 LYD778 85053.1 — — — — — — 0.546 0.26 13LYD778 85053.2 — — — 13.7 0.13 28 0.608 0.02 26 LYD778 85053.4 — — —13.2 0.17 24 0.533 0.28 11 LYD772 84526.1 — — — 13.1 0.20 22 0.555 0.1715 LYD772 84529.2 — — — — — — 0.536 0.26 11 LYD730 84258.1 — — — — — —0.577 0.07 20 LYD711 85315.3 — — — 14.1 0.10 32 0.575 0.08 19 LYD71185316.3 — — — 13.8 0.11 29 0.573 0.09 19 LYD711 85316.5 — — — 13.8 0.1129 0.588 0.04 22 CONT. — 0.677 — — 10.7 — — 0.482 — — LGP1 76250.4 0.7350.19 10 — — — — — — CONT. — 0.669 — — — — — — — — LGP71 82500.4 0.6880.13 27 — — — — — — LGP71 82502.4 0.690 0.11 27 — — — — — — LGP7182503.1 0.658 0.01 21  7.79 0.27  7 — — — LGP71 82503.2 0.682 0.13 26 —— — — — — CONT. — 0.542 — —  7.27 — — — — — LGP1 76249.3 0.689 0.30  6 —— — — — — LGP1 76250.3 0.725 0.18 12 — — — — — — CONT. — 0.649 — — — — —— — — LGP34 75739.3 — — — 11.3 0.05 12 — — — CONT. — — — — 10.1 — — — —— LYD922 83823.5 0.804 0.25 13 — — — — — — LYD915 84657.1 — — — 14.90.21 21 0.656 0.14 18 LYD913 84195.1 — — — 14.8 0.23 20 0.630 0.25 13LYD899 83721.2 0.816 0.21 14 — — — — — — LYD893 83951.1 0.825 0.18 15 —— — — — — LYD893 83952.6 0.803 0.29 12 — — — — — — LYD848 84289.1 0.8200.20 15 15.8 0.10 29 — — — LYD840 84085.2 0.812 0.24 14 14.8 0.23 20 — —— LYD833 83511.4 0.803 0.26 12 — — — — — — LYD833 83512.2 0.805 0.28 13— — — — — — LYD833 83513.5 — — — 16.1 0.09 31 — — — LYD789 84132.2 0.8100.24 13 — — — — — — LYD746 83901.5 0.821 0.18 15 — — — — — — LYD71784356.2 0.807 0.24 13 — — — — — — CONT. — 0.715 — — 12.3 — — 0.558 — —LYD919 83642.2 0.824 0.07 20 12.5 0.23 18 0.598 0.04 18 LYD919 83644.3 —— — — — — 0.573 0.14 13 LYD919 83646.1 — — — — — — 0.567 0.19 12 LYD900 83738.10 0.773 0.25 12 — — — — — — LYD900  83738.11 0.806 0.12 17 — — —— — — LYD898 83641.6 0.773 0.23 12 — — — — — — LYD894 84361.1 0.771 0.2712 — — — — — — LYD886 83634.2 0.772 0.24 12 — — — — — — LYD886 83636.10.870 0.02 26 — — — 0.556 0.25 10 LYD883 83912.3 — — — 13.3 0.10 250.590 0.07 17 LYD882 84065.1 0.815 0.10 18 — — — — — — LYD871 83716.2 —— — 12.5 0.23 17 — — — LYD871 83716.4 0.766 0.27 11 — — — — — — LYD87183718.6 — — — 12.9 0.14 22 0.555 0.25  9 LYD865 83731.1 — — — 13.4 0.0926 0.572 0.14 13 LYD839 83521.1 0.769 0.29 12 — — — — — — LYD811 83713.30.772 0.24 12 12.6 0.21 18 0.587 0.07 16 LYD793 83499.7 — — — — — —0.571 0.14 13 LYD777 83489.3 0.835 0.05 21 12.6 0.21 18 — — — LYD77783492.3 0.778 0.20 13 — — — — — — LYD772 84529.2 0.774 0.22 12 — — —0.557 0.24 10 LYD772 84529.3 — — — 12.3 0.29 16 — — — LYD748 84919.10.792 0.15 15 — — — — — — LYD747 85011.3 0.773 0.25 12 — — — — — —LYD745 84262.1 — — — — — — 0.555 0.29 10 LYD745 84263.1 — — — — — —0.565 0.19 12 LYD745 84264.2 0.771 0.24 12 — — — — — — CONT. — 0.688 — —10.6 — — 0.507 — — LGP9 75515.1 0.684 0.02 17 — — — — — — LGP44 75763.30.640 0.26  9 — — — — — — LGP44 75765.3 0.700 0.02 20 — — — — — — LGP1075385.3 0.734 0.03 25 — — — — — — CONT. — 0.585 — — — — — — — — LGP4677258.3 0.644 0.07 12 — — — — — — LGP46 77259.3 0.645 0.14 12 — — — — —— LGP46 77259.6 0.606 0.27  5 — — — — — — LGP45 77196.6 0.660 0.15 15 —— — — — — LGP45 77197.4 0.637 0.25 11 — — — — — — LGP19 76940.2 0.6030.07  5 — — — — — — CONT. — 0.576 — — — — — — — — LGP48 77204.6 0.7860.29  6 — — — — — — CONT. — 0.739 — — — — — — — — Table 175.“CONT.”—Control; “Ave.”—Average; “% Incr.” = % increment;“p-val.”—p-value, L- p < 0.01. RGR = relative growth rate.

TABLE 176 Genes showing improved plant performance at Normal growthconditions under regulation of At6669 promoter Rosette Diameter HarvestIndex Rosette Area [cm²] [cm] Gene P- % P- % P- % Name Event # Ave. Val.Incr. Ave. Val. Incr. Ave. Val. Incr. LGP77 81452.2 — — —  7.03 0.06 184.78 0.02 8 LGP77 81453.3 0.254 0.28  9 — — — — — — LGP77 81456.3 — — —— — — 4.59 0.17 3 CONT. — 0.234 — —  5.97 — — 4.44 — — LGP52 76963.1 — —— 11.6 0.23  9 5.72 0.13 6 LGP52 76965.2 — — — 11.5 0.24  8 5.65 0.27 5CONT. — — — — 10.6 — — 5.38 — — LGP58 76972.1 0.340 0.14 14 — — — — — —LGP47 76957.1 0.334 0.17 12 — — — — — — LGP47 76960.3 0.342 0.08 15 — —— — — — CONT. — 0.298 — — — — — — — — LYD930 83833.4 0.396 L 30 — — — —— — LYD930 83834.3 — — — — — — 5.97 0.24 4 LYD881 84058.5 — — — 13.30.23 10 6.15 0.13 8 LYD877 83630.3 — — — 15.0 L 24 6.54 L 14  LYD87783630.4 — — — 14.1 0.13 16 6.32 0.07 11  LYD863 83810.7 — — — — — — 6.220.28 9 LYD846 83531.4 — — — 13.0 0.29  8 6.06 0.13 6 LYD846 83533.10.348 0.19 14 — — — — — — LYD831 83803.1 — — — 13.1 0.25  8 6.14 0.06 7LYD831 83803.3 — — — 13.4 0.15 11 6.14 0.06 7 LYD831 83803.5 — — — 13.10.26  8 6.07 0.10 6 LYD788 83798.4 — — — 14.9 0.12 23 6.49 0.03 13 LYD788 83800.4 0.337 0.21 10 — — — — — — LYD788 83800.5 — — — 13.6 0.1013 6.19 0.08 8 LYD783 84170.1 0.368 0.02 21 — — — — — — LYD783 84170.30.371 0.13 22 13.8 0.08 14 6.12 0.10 7 LYD779 83704.2 — — — 13.6 0.10 126.11 0.08 7 LYD779 83708.2 — — — 13.9 0.06 15 6.29 0.02 10  LYD77983708.4 — — — — — — 6.24 0.19 9 LYD776 83944.1 0.361 0.16 18 — — — — — —LYD776 83947.1 — — — 13.2 0.25  9 6.09 0.18 7 LYD776 83947.6 0.329 0.29 8 — — — — — — LYD764 83479.4 — — — 15.1 0.06 25 6.67 L 17  LYD76483480.1 — — — — — — 6.29 0.22 10  LYD731 83456.1 — — — 14.0 0.24 15 6.250.17 9 LYD731 83458.1 — — — — — — 6.06 0.19 6 LYD715 84155.5 — — — — — —6.00 0.21 5 LYD715 84158.1 — — — — — — 6.17 0.20 8 LYD715 84158.3 — — —14.0 0.05 15 6.21 0.03 9 LYD713 83786.4 0.351 0.19 15 14.3 0.17 18 — — —LYD713 83788.3 — — — 15.0 L 24 6.41 L 12  LYD710 83895.3 — — — — — —6.15 0.29 8 LYD710 83895.6 — — — 14.4 0.03 19 6.35 0.04 11  LYD71083896.1 — — — 14.0 0.21 16 6.16 0.20 8 LYD708 83451.6 — — — — — — 6.090.12 7 LYD708 83451.7 — — — 14.1 0.21 17 6.36 0.14 11  LYD700 84151.1 —— — — — — 6.11 0.12 7 LYD700 84151.4 0.378 0.01 24 — — — — — — LYD69883780.4 — — — 14.0 0.04 16 6.20 0.04 8 CONT. — 0.305 — — 12.1 — — 5.72 —— LGP77 81452.2 — — —  5.22 0.20 12 4.32 0.24 8 LGP77 81453.3 — — — 4.94 0.16  6 4.13 0.30 3 CONT. — — — —  4.64 — — 4.00 — — LGP73 81449.7— — — — — — 4.66 0.15 3 LGP73 81449.8 — — —  8.66 L 24 5.01 L 11  CONT.— — — —  7.00 — — 4.51 — — LYD930 83832.3 — — — 10.2 0.24 26 5.25 0.2012  LYD930 83834.3 — — —  9.54 0.13 18 5.01 0.19 7 LYD881 84058.2 — — —— — — 4.95 0.13 6 LYD877 83631.2 0.326 0.13 18 — — — — — — LYD86383810.7 — — —  9.53 0.05 17 4.99 0.26 7 LYD846 83531.3 — — —  8.81 0.29 9 — — — LYD831 83803.3 — — —  9.37 0.07 15 5.09 0.04 9 LYD831 83803.50.333 0.02 21 — — — — — — LYD831 83803.6 0.319 0.10 16 — — — — — —LYD788 83800.4 0.316 0.11 15 10.2 0.01 25 5.28 L 13  LYD788 83800.50.342 L 24 — — — — — — LYD783 84170.1 — — —  9.32 0.22 15 5.04 0.11 8LYD783 84170.3 — — —  8.95 0.24 10 — — — LYD783 84172.2 0.317 0.07 15 —— — — — — LYD779 83704.2 — — —  9.36 0.07 15 4.96 0.13 6 LYD779 83708.2— — —  9.07 0.18 12 — — — LYD776 83947.4 0.304 0.14 10 — — — — — —LYD764 83479.4 — — —  9.03 0.15 11 4.97 0.20 6 LYD764 83483.1 — — — 9.82 0.03 21 5.10 0.03 9 LYD740 83462.1 — — —  8.82 0.26  9 4.93 0.16 5LYD731 83456.1 0.363 0.04 31 — — — — — — LYD715 84155.5 — — — 10.7 0.1032 5.43 0.12 16  LYD715 84158.1 — — — 10.4 0.29 29 — — — LYD715 84158.3— — —  9.02 0.16 11 4.93 0.16 5 LYD713 83788.3 — — —  9.04 0.15 11 — — —LYD713 83789.3 0.359 0.25 30  8.94 0.25 10 — — — LYD708 83451.5 0.3290.24 19 — — — — — — LYD698 83776.2 0.313 0.24 13 — — — — — — LYD69883780.3 0.373 0.13 35 — — — — — — CONT. — 0.276 — —  8.12 — — 4.68 — —LGP49 77652.6 — — — 14.2 0.22 11 — — — CONT. — — — — 12.8 — — — — —LYD919 83642.2 — — — 11.4 0.09 33 5.69 0.02 18  LYD919 83644.3 — — — 9.36 0.22  9 — — — LYD919 83645.1 0.334 0.28  9  9.79 0.07 14 5.08 0.175 LYD913 84195.2 — — —  9.48 0.27 11 — — — LYD913 84198.4 — — —  9.640.08 12 — — — LYD913 84198.7 0.359 0.04 17 10.6 0.24 24 — — — LYD90984174.2 — — — 11.3 0.15 31 5.43 0.05 12  LYD909 84174.4 — — — 11.6 L 355.45 L 13  LYD909 84177.1 — — — 10.2 0.02 19 5.32 0.02 10  LYD90984178.3 — — —  9.95 0.03 16 5.14 0.22 6 LYD900  83738.10 — — — 11.0 0.0629 5.46 0.02 13  LYD900  83738.14 — — — 10.7 0.09 24 5.41 0.07 12 LYD900 83738.8 — — — 12.4 0.18 44 5.95 0.14 23  LYD898 83640.1 — — —11.3 0.22 32 5.48 0.20 13  LYD898 83641.5 — — — — — — 5.06 0.27 4 LYD89883641.6 — — — 10.2 0.02 19 5.17 0.08 7 LYD898 83641.8 — — — — — — 5.100.24 5 LYD896 83659.5 — — —  9.59 0.16 12 5.20 0.06 8 LYD896 83661.2 — ——  10.00 0.10 17 5.13 0.29 6 LYD896 83661.4 — — — 10.1 0.02 18 5.32 0.0310  LYD895 83535.4 — — — 10.5 0.10 23 5.19 0.16 7 LYD893 83951.1 0.3320.26  8 11.1 L 29 5.39 0.01 11  LYD893 83952.5 — — — 10.8 0.02 26 5.52 L14  LYD893 83952.6 — — — 10.7 0.25 25 5.24 0.23 8 LYD893 83952.7 — — —10.5 0.14 23 5.42 0.05 12  LYD886 83634.2 — — — — — — 5.26 0.19 9 LYD88683635.4 0.343 0.21 12 10.5 0.03 23 5.43 0.12 12  LYD886 83636.1 — — —10.2 0.19 19 — — — LYD882 84061.1 — — — 11.3 0.04 32 5.60 L 16  LYD88284064.4 — — — 10.3 0.10 20 5.20 0.06 7 LYD882 84065.7 — — — 10.4 0.08 21— — — LYD871 83715.4 — — —  9.66 0.07 13 5.22 0.06 8 LYD871 83716.2 — ——  9.71 0.07 13 5.30 0.10 9 LYD871 83716.4 — — — — — — 5.17 0.24 7LYD871 83718.6 — — —  9.79 0.07 14 5.19 0.06 7 LYD848 84290.3 — — — 11.6L 35 5.54 L 14  LYD848 84290.4 — — — 11.1 0.29 29 5.33 0.26 10  LYD84884292.5 — — — 10.7 L 25 5.40 0.01 12  LYD840 84085.2 — — —  9.57 0.19 125.15 0.12 7 LYD840 84085.4 — — —  9.46 0.13 10 5.10 0.18 5 LYD78684582.2 — — —  9.42 0.17 10 — — — LYD786 84584.4 — — —  9.57 0.15 125.11 0.29 6 LYD786 84585.3 — — — — — — 5.13 0.11 6 LYD786 84585.4 — — —10.0 0.04 17 5.28 0.04 9 LYD746 83898.2 — — — 10.6 L 24 5.30 0.03 10 LYD746 83902.2 — — — 11.4 0.14 33 5.53 0.28 14  LYD746 83902.4 — — —10.4 0.01 21 5.28 0.04 9 LYD745 84261.1 — — — 10.1 0.16 18 — — — LYD74584261.4 — — — 11.0 L 29 5.51 L 14  LYD745 84262.1 — — — 13.1 L 53 5.88 L21  LYD745 84264.2 0.349 0.08 14 10.4 0.01 21 5.39 0.22 11  LYD73383766.2 — — —  9.46 0.14 10 5.06 0.20 5 LYD733 83766.5 — — — — — — 5.100.14 5 LYD733 83768.3 0.351 0.07 14 11.2 L 30 5.46 L 13  LYD717 84353.1— — —  9.75 0.09 14 5.14 0.11 6 LYD717 84354.2 — — —  9.55 0.10 11 5.090.15 5 LYD717 84356.2 — — — 11.6 L 35 5.52 L 14  CONT. — 0.307 — —  8.57— — 4.84 — — LGP46 77260.2 0.414 0.03 18 — — — — — — LGP19 76939.2 0.3760.22  7 — — — — — — LGP19 76940.1 0.377 0.20  7 — — — — — — CONT. —0.351 — — — — — — — — LGP32 75397.4 0.225 0.03 25 10.2 0.08 20 5.62 0.0511  LGP12 78567.3 — — — — — — 5.37 0.23 6 CONT. — 0.180 — —  8.44 — —5.06 — — LGP74 81328.3 — — — 11.8 0.06 18 5.60 0.15 7 CONT. — — — — 9.97 — — 5.24 — — LGP43 76951.2 0.275 0.28  9 — — — — — — LGP43 76953.20.283 0.12 12 — — — — — — CONT. — 0.253 — — — — — — — — LGP74 81325.1 —— —  9.66 0.20  8 5.53 0.12 4 LGP74 81326.4 0.352 0.07 26 — — — — — —LGP74 81328.3 — — — 10.6 0.15 19 5.81 0.12 9 CONT. — 0.281 — —  8.92 — —5.34 — — LGP71 82503.1 — — —  8.52 0.06 38 5.29 0.12 18  CONT. — — — — 6.19 — — 4.50 — — LYD911 86503.1 — — — 12.7 0.04 21 5.94 0.16 7 LYD90784976.1 — — — 12.0 0.10 14 6.02 0.08 8 LYD904 84497.2 — — — 11.8 0.11 125.94 0.18 7 LYD904 84499.2 — — — 14.0 L 33 6.37 L 15  LYD902 84948.5 — —— 13.2 0.28 25 6.36 0.21 14  LYD899 83723.8 — — — — — — 6.03 0.18 8LYD867 85536.5 — — — 11.4 0.24  8 5.96 0.05 7 LYD844 85192.1 — — — 11.70.16 12 6.00 0.04 8 LYD844 85192.3 — — — — — — 6.08 0.26 9 LYD84485192.7 — — — 12.4 0.03 18 5.99 0.04 8 LYD825 85883.1 — — — 12.5 0.02 196.00 0.04 8 LYD825 85884.2 — — — 12.4 0.03 18 5.95 0.08 7 LYD812 85560.1— — — 11.4 0.25  9 — — — LYD812 85560.2 — — — 13.4 L 28 6.27 0.01 13 LYD812 85564.1 — — — 11.8 0.30 12 — — — LYD778 85053.2 — — — — — — 6.580.18 18  LYD778 85053.3 — — — 11.5 0.21  9 5.93 0.07 7 LYD778 85053.4 —— — 12.9 0.14 23 5.95 0.06 7 LYD772 84526.1 — — — 12.7 0.29 21 — — —LYD772 84529.2 — — — — — — 6.04 0.03 9 LYD718 85457.1 — — — — — — 6.070.08 9 LYD711 85315.3 — — — — — — 6.31 0.30 14  LYD711 85316.3 — — —13.4 0.25 27 6.29 0.25 13  LYD711 85316.5 — — — 13.6 0.21 29 6.49 0.1617  CONT. — — — — 10.5 — — 5.56 — — LGP71 82503.1 — — —  6.15 0.13 104.52 0.17 6 CONT. — — — —  5.57 — — 4.26 — — LGP1 76248.1 0.371 0.27  9— — — — — — LGP1 76249.3 0.367 0.22  7 — — — — — — CONT. — 0.341 — — — —— — — — LYD929 83647.2 0.353 0.15 10 — — — — — — LYD929 83651.2 — — —13.3 0.12 10 — — — LYD922 83823.6 — — — 13.3 0.11 11 — — — LYD91584657.1 — — — 14.3 0.30 19 6.92 0.11 14  LYD915 84658.1 0.381 0.02 19 —— — — — — LYD915 84659.1 0.367 0.30 14 — — — — — — LYD913 84195.1 — — —14.3 0.03 19 6.76 0.10 12  LYD913 84198.1 0.344 0.30  7 — — — — — —LYD913 84198.4 0.347 0.26  8 — — — — — — LYD909 84174.1 — — — 13.7 0.2214 — — — LYD909 84177.1 0.359 0.10 12 — — — — — — LYD899 83722.1 0.3660.06 14 — — — — — — LYD895 83535.3 0.367 0.06 14 — — — — — — LYD89583537.3 0.378 0.04 18 — — — — — — LYD895 83537.4 0.363 0.28 13 — — — — —— LYD893 83950.1 — — — 13.5 0.24 12 — — — LYD893 83952.5 — — — 13.4 0.0912 — — — LYD848 84289.1 — — — 15.2 0.07 26 6.66 0.10 10  LYD840 84085.2— — — 14.3 0.02 19 6.53 0.22 8 LYD833 83511.1 0.365 0.10 14 — — — — — —LYD833 83513.5 — — — 15.6 L 30 6.60 0.03 9 LYD821 84054.2 — — — 12.90.25  7 — — — LYD821 84054.5 0.355 0.14 11 — — — — — — LYD789 84132.3 —— — 12.8 0.28  7 — — — LYD733 83768.1 0.376 0.03 17 — — — — — — LYD71784356.2 0.400 0.02 25 — — — — — — LYD704 83785.2 — — — — — — 6.29 0.27 4LYD704 83785.5 0.425 0.05 32 — — — — — — CONT. — 0.321 — — 12.0 — — 6.05— — LGP52 76963.1 — — — 13.0 0.28 12 6.00 0.17 7 CONT. — — — — 11.6 — —5.59 — — LYD919 83642.2 — — — 12.0 L 17 6.18 0.02 12  LYD919 83644.3 — —— 11.2 0.28  9 5.98 0.18 9 LYD919 83646.1 — — — 11.4 0.20 11 — — —LYD898 83641.5 — — — 11.3 0.24 10 5.96 0.07 8 LYD898 83641.8 0.379 0.2218 11.7 0.14 14 — — — LYD894 84361.1 — — — — — — 5.69 0.15 3 LYD89484362.1 0.359 0.17 12 — — — — — — LYD894 84362.2 0.364 0.28 14 10.9 0.11 7 5.67 0.09 3 LYD894 84362.3 — — — — — — 5.61 0.25 2 LYD886 83634.2 — —— 10.9 0.17  6 5.64 0.14 3 LYD886 83634.3 0.380 0.08 19 11.0 0.26  7 — —— LYD886 83636.1 — — — 11.6 L 14 5.88 0.07 7 LYD886 83636.3 0.353 0.2410 — — — — — — LYD883 83911.4 — — — — — — 5.63 0.28 2 LYD883 83912.3 — —— 12.7 L 24 6.28 L 14  LYD882 84064.4 0.371 0.25 16 — — — — — — LYD88284065.1 — — — 11.3 0.06 10 5.83 0.17 6 LYD871 83716.2 0.379 0.06 18 12.00.03 17 5.86 0.18 7 LYD871 83718.6 — — — 12.5 0.09 22 6.12 L 11  LYD86583731.1 — — — 12.9 0.10 26 6.17 0.19 12  LYD865 83733.5 — — — 11.0 0.09 8 5.65 0.15 3 LYD839 83522.1 — — — 10.7 0.30  4 — — — LYD811 83711.4 —— — 11.0 0.29  8 5.73 0.05 4 LYD811 83713.3 — — — 12.0 0.11 17 6.04 0.1210  LYD793 83499.2 — — — 11.5 0.02 12 5.88 0.06 7 LYD793 83499.7 — — —11.1 0.07  8 — — — LYD793 83500.4 0.367 0.10 15 — — — — — — LYD78684582.1 0.360 0.16 12 — — — — — — LYD786 84582.2 0.356 0.26 11 — — — — —— LYD777 83489.3 — — — 12.1 L 18 5.92 L 8 LYD777 83492.3 — — — 11.1 0.06 8 — — — LYD777 83493.3 — — — 10.7 0.25  5 — — — LYD772 84526.1 — — —10.8 0.14  6 5.61 0.25 2 LYD772 84529.1 0.368 0.16 15 — — — — — — LYD77284529.2 — — — 11.5 0.21 12 5.85 L 6 LYD772 84529.3 0.361 0.20 12 — — — —— — LYD748 84918.3 — — — — — — 5.64 0.15 2 LYD748 84919.4 — — — — — —5.69 0.15 3 LYD747 85011.1 — — — — — — 5.84 0.18 6 LYD747 85011.3 — — —10.7 0.25  5 5.67 0.09 3 LYD747 85014.1 — — — — — — 5.61 0.25 2 LYD74584261.1 — — — 11.2 0.12  9 5.73 0.04 4 LYD745 84262.1 — — — 11.8 0.10 165.97 L 9 LYD745 84263.1 — — — 11.7 0.05 14 6.15 L 12  CONT. — 0.321 — —10.2 — — 5.50 — — LGP46 77258.3 0.354 0.20  8 — — — — — — CONT. — 0.327— — — — — — — — LGP47 76956.1 0.350 0.13 17 — — — — — — CONT. — 0.300 —— — — — — — — Table 176. “CONT.”—Control; “Ave.”—Average; “% Incr.” = %increment; “p-val.”—p-value, L- p < 0.01.

TABLE 177 Genes showing improved plant performance at Normal growthconditions under regulation of At6669 promoter 1000 Seed Weight [mg]Gene Seed Yield [mg] % Name Event # Ave. P-Val. % Incr. Ave. P-Val.Incr. LGP54 77039.1 — — — 22.4 0.09  5 LGP53 76966.2 — — — 25.7 L 20LGP53 76968.1 — — — 26.1 L 22 LGP52 76962.1 — — — 26.6 L 25 LGP5276963.1 — — — 23.9 0.06 12 LGP52 76965.2 — — — 26.0 L 22 CONT. — — — —21.3 — — LGP58 76972.1 344.0 0.20 19 — — — LGP58 76975.5 — — — 21.0 0.12 5 LGP48 77202.1 354.5 0.05 23 21.1 0.08  6 LGP48 77202.4 320.2 0.28 11— — — LGP48 77203.2 345.9 0.23 20 — — — LGP48 77204.3 — — — 22.4 L 12LGP48 77204.6 337.4 0.29 17 — — — LGP47 76960.3 347.1 0.07 20 — — —CONT. — 289.0 — — 20.0 — — LYD930 83831.3 — — — 27.9 0.22 22 LYD93083832.3 — — — 27.2 L 20 LYD930 83833.4 518.1 0.27 18 — — — LYD88184058.5 537.8 0.14 22 — — — LYD877 83630.2 — — — 26.0 L 14 LYD87783630.3 — — — 25.7 0.01 13 LYD863 83808.4 — — — 27.6 0.11 21 LYD86383810.7 — — — 26.6 0.12 17 LYD846 83533.4 — — — 27.1 0.15 19 LYD78883798.3 479.1 0.26  9 — — — LYD788 83798.4 — — — 25.2 0.27 11 LYD78384170.1 506.9 0.06 15 24.5 0.07  8 LYD783 84170.3 505.3 0.07 15 — — —LYD783 84172.2 — — — 24.2 0.11  6 LYD779 83704.2 — — — 26.9 L 18 LYD77683944.1 592.4 0.23 35 — — — LYD776 83947.6 514.5 0.04 17 24.0 0.20  5LYD764 83479.4 — — — 26.0 0.28 14 LYD764 83483.6 — — — 25.7 0.27 13LYD731 83456.1 — — — 24.3 0.12  7 LYD713 83788.3 — — — 25.4 0.29 12LYD710 83895.3 — — — 26.7 0.09 17 LYD710 83895.6 — — — 28.3 0.12 24LYD708 83451.7 — — — 24.4 0.09  7 LYD700 84149.4 — — — 24.2 0.22  6LYD700 84150.3 — — — 28.6 0.14 26 LYD700 84151.4 498.8 0.09 13 — — —LYD698 83778.1 — — — 26.7 0.17 17 LYD698 83780.3 — — — 24.9 0.08  9LYD698 83780.4 487.8 0.26 11 — — — CONT. — 440.0 — — 22.8 — — LGP7781453.3 — — — 21.9 0.05 12 CONT. — — — — 19.5 — — LGP73 81449.3 390.30.28 18 — — — LGP73 81449.8 373.7 0.12 13 24.8 L 32 CONT. — 330.5 — —18.7 — — LYD930 83831.3 — — — 23.4 0.17 17 LYD930 83832.3 — — — 24.10.12 21 LYD881 84058.5 — — — 21.5 0.29  8 LYD877 83630.3 — — — 24.1 0.0521 LYD863 83808.4 357.6 0.21 11 22.2 L 12 LYD863 83810.6 — — — 24.4 0.1623 LYD846 83529.5 — — — 20.6 0.28  4 LYD846 83531.4 — — — 20.9 0.27  5LYD831 83803.5 404.6 0.11 26 — — — LYD831 83803.6 394.3 0.02 23 — — —LYD788 83798.4 — — — 23.4 0.14 17 LYD788 83800.1 348.2 0.26  9 — — —LYD788 83800.4 361.8 0.14 13 21.6 0.09  9 LYD788 83800.5 413.1 L 29 — —— LYD783 84172.2 408.8 L 27 — — — LYD779 83704.2 373.6 0.05 16 — — —LYD779 83708.4 415.9 0.12 30 21.0 0.28  6 LYD776 83944.1 351.5 0.22 10 —— — LYD764 83479.4 — — — 23.8 L 20 LYD740 83461.4 358.3 0.15 12 — — —LYD731 83456.1 413.9 0.08 29 — — — LYD731 83456.3 — — — 21.1 0.27  6LYD715 84158.1 — — — 23.7 0.17 19 LYD713 83788.3 — — — 23.7 L 19 LYD71383789.3 434.4 0.20 35 — — — LYD708 83451.5 366.5 0.20 14 — — — LYD69883778.1 — — — 21.4 0.06  8 LYD698 83780.3 429.0 0.01 34 — — — CONT. —320.8 — — 19.9 — — LGP49 77651.8 — — — 20.8 0.15  4 LGP49 77652.6 — — —24.6 0.06 23 CONT. — — — — 20.0 — — LYD919 83644.2 390.9 0.08 13 — — —LYD913 84198.7 424.2 0.01 23 — — — LYD909 84174.1 — — — 20.2 0.29  7LYD898 83641.5 — — — 22.3 0.01 18 LYD896 83659.2 — — — 23.9 0.06 27LYD895 83535.5 403.5 0.04 17 — — — LYD886 83635.4 400.2 0.30 16 — — —LYD882 84065.1 — — — 19.6 0.30  4 LYD840 84085.2 — — — 21.5 L 14 LYD78684582.1 396.1 0.27 15 — — — LYD745 84262.1 375.5 0.22  9 — — — LYD73383766.5 375.8 0.24  9 — — — LYD733 83768.3 376.2 0.24  9 — — — LYD71784353.1 392.3 0.21 14 — — — CONT. — 345.3 — — 18.8 — — LGP45 77196.1 — —— 24.5 L 18 CONT. — — — — 20.8 — — LGP32 75397.4 178.8 0.05 26 — — —CONT. — 141.9 — — — — — LGP74 81326.1 — — — 25.6 0.08 10 LGP74 81328.3 —— — 24.9 0.28  8 CONT. — — — — 23.2 — — LGP43 76951.2 304.6 0.27 11 —LNU824- — LGP43 76955.2 — — — 22.9 0.04 15 CONT. — 274.9 — — 20.0 — —LGP74 81328.3 — — — 22.6 0.02 13 CONT. — — — — 19.9 — — LGP71 82500.4 —— — 24.8 0.10 15 LGP71 82503.1 — — — 25.8 0.02 19 LGP71 82503.2 — — —23.7 0.10 10 CONT. — — — — 21.7 — — LGP73 81449.8 — — — 28.2 0.04 18CONT. — — — — 23.8 — — LGP71 82500.4 — — — 23.7 L 25 LGP71 82503.1 — — —23.4 0.02 24 CONT. — — — — 19.0 — — LGP34 75739.3 — — — 24.8 0.08 10CONT. — — — — 22.5 — — LYD915 84658.1 473.2 0.15 23 — — — LYD913 84195.4— — — 23.7 L 12 LYD909 84177.1 444.8 0.21 16 — — — LYD899 83722.1 420.10.23  9 — — — LYD895 83535.5 427.3 0.20 11 — — — LYD895 83537.3 445.90.23 16 — — — LYD848 84292.5 — — — 23.1 0.22  9 LYD840 84085.2 — — —25.4 0.02 20 LYD833 83511.1 430.5 0.11 12 22.7 0.07  8 LYD789 84131.3448.0 0.12 16 — — — LYD733 83768.1 428.4 0.12 11 — — — LYD717 84356.2463.2 0.02 20 — — — LYD704 83785.5 469.4 0.01 22 — — — CONT. — 384.7 — —21.2 — — LGP54 77039.1 — — — 22.6 L  8 LGP53 76966.2 — — — 25.9 L 23LGP53 76968.1 — — — 25.3 0.03 21 LGP53 76968.4 — — — 21.9 0.18  4 LGP5276962.1 — — — 25.1 L 19 LGP52 76963.1 423.6 0.27 14 24.5 L 16 LGP5276963.3 — — — 21.8 0.12  4 LGP52 76965.2 — — — 24.9 L 19 CONT. — 370.5 —— 21.0 — — LGP34 75737.4 — — — 21.6 0.13  5 LGP34 75739.3 — — — 24.6 L20 CONT. — — — — 20.6 — — LYD919 83646.1 — — — 22.2 0.18 12 LYD90083738.8 — — — 23.1 0.01 17 LYD898 83641.5 — — — 25.6 0.21 29 LYD89883641.8 451.3 0.13 10 — — — LYD894 84362.2 458.6 0.13 12 — — — LYD89484362.3 — — — 20.6 0.09  4 LYD886 83634.3 509.9 0.07 25 — — — LYD88683636.3 500.2 0.25 22 20.9 0.05  5 LYD883 83911.2 454.4 0.12 11 — — —LYD883 83912.3 444.7 0.20  9 — — — LYD882 84064.4 442.3 0.22  8 — — —LYD871 83716.2 453.1 0.17 11 — — — LYD871 83718.6 — — — 20.6 0.08  4LYD865 83730.1 — — — 22.8 0.26 15 LYD865 83733.5 444.7 0.22  9 — — —LYD839 83521.1 — — — 24.6 L 24 LYD839 83522.1 — — — 23.1 L 17 LYD79383499.7 — — — 23.0 L 16 LYD786 84582.1 463.9 0.07 14 — — — LYD77783489.3 — — — 20.3 0.29  3 LYD772 84529.1 481.7 0.16 18 — — — LYD77284529.2 — — — 24.6 L 24 LYD747 85011.3 — — — 21.8 0.12 10 LYD745 84262.1— — — 21.9 0.11 10 CONT. — 408.6 — — 19.8 — — LGP44 75764.8 — — — 23.40.04 14 LGP44 75765.3 — — — 21.0 0.13  2 CONT. — — — — 20.5 — — LGP4677256.1 — — — 20.9 0.25  6 LGP45 77196.1 — — — 24.7 L 25 LGP19 76938.3303.6 0.15 17 — — — LGP19 76939.1 — — — 20.4 0.27  4 CONT. — 259.9 — —19.7 — — LGP48 77204.3 — — — 23.5 0.01 13 LGP47 76956.1 316.7 0.21 14 —— — CONT. — 277.7 — — 20.8 — — Table 177. “CONT.”—Control;“Ave.”—Average; “% Incr.” = % increment; “p-val.”—p-value, L- p < 0.01.

Example 27 Evaluation of Transgenic Arabidopsis for Seed Yield and PlantGrowth Rate Under Normal Conditions in Greenhouse Assays Until Bolting(GH-SB Assays)

Assay 2: Plant Performance Improvement Measured Until Bolting Stage:Plant Biomass and Plant Growth Rate Under Normal Greenhouse Conditions(GH-SB Assays)—

This assay follows the plant biomass formation and the rosette areagrowth of plants grown in the greenhouse under normal growth conditions.Transgenic Arabidopsis seeds were sown in agar media supplemented with ½MS medium and a selection agent (Kanamycin). The T₂ transgenic seedlingswere then transplanted to 1.7 trays filled with peat and perlite in a1:1 ratio. Plants were grown under normal conditions which includedirrigation of the trays with a solution containing of 6 mM inorganicnitrogen in the form of KNO₃ with 1 mM KH₂PO₄, 1 mM MgSO₄, 2 mM CaCl₂and microelements. Under normal conditions the plants grow in acontrolled environment in a closed transgenic greenhouse; temperaturewas 18-22° C., humidity around 70%; Irrigation was done by flooding witha water solution containing 6 mM N (nitrogen) (as describedhereinabove), and flooding was repeated whenever water loss reached 50%.All plants were grown in the greenhouse until bolting stage. Plantbiomass (the above ground tissue) was weighted directly after harvestingthe rosette (plant fresh weight [FW]). Following plants were dried in anoven at 50° C. for 48 hours and weighted (plant dry weight [DW]).

Each construct was validated at its T₂ generation. Transgenic plantstransformed with a construct conformed by an empty vector carrying theAt6669 promoter (SEQ ID NO: 15751) and the selectable marker, were usedas control. Additionally or alternatively, Mock-transgenic plantsexpressing the uidA reporter gene (GUS-Intron) or with no gene at all,under the same promoter were used as control.

The plants were analyzed for their overall size, growth rate, freshweight and dry matter. Transgenic plants performance was compared tocontrol plants grown in parallel under the same conditions. Theexperiment was planned in nested randomized plot distribution. For eachgene of the invention three to five independent transformation eventswere analyzed from each construct.

Digital imaging—A laboratory image acquisition system, which consists ofa digital reflex camera (Canon EOS 300D) attached with a 55 mm focallength lens (Canon EF-S series), mounted on a reproduction device(Kaiser RS), which includes 4 light units (4×150 Watts light bulb) wasused for capturing images of plant samples.

The image capturing process was repeated every 2 days starting from day1 after transplanting till day 15. Same camera, placed in a custom madeiron mount, was used for capturing images of larger plants sawn in whitetubs in an environmental controlled greenhouse. The tubs were squareshape include 1.7 liter trays. During the capture process, the tubeswere placed beneath the iron mount, while avoiding direct sun light andcasting of shadows.

An image analysis system was used, which consists of a personal desktopcomputer (Intel P4 3.0 GHz processor) and a public domain program—ImageJ1.39 [Java based image processing program which was developed at theU.S. National Institutes of Health and freely available on the internetat rsbweb (dot) nih (dot) gov/]. Images were captured in resolution of10 Mega Pixels (3888×2592 pixels) and stored in a low compression JPEG(Joint Photographic Experts Group standard) format. Next, analyzed datawas saved to text files and processed using the JMP statistical analysissoftware (SAS institute).

Leaf analysis—Using the digital analysis leaves data was calculated,including leaf number, rosette area, rosette diameter, and leaf bladearea.

Vegetative growth rate: the relative growth rate (RGR) of leaf number(Formula VIII, described above), rosette area (Formula IX describedabove) and plot coverage (Formula XI, described above) were calculatedusing the indicated formulas.

Plant Fresh and Dry weight—On about day 80 from sowing, the plants wereharvested and directly weight for the determination of the plant freshweight (FW) and left to dry at 50° C. in a drying chamber for about 48hours before weighting to determine plant dry weight (DW).

Statistical analyses—To identify outperforming genes and constructs,results from the independent transformation events tested were analyzedseparately. Data was analyzed using Student's t-test and results wereconsidered significant if the p value was less than 0.1. The JMPstatistics software package was used (Version 5.2.1, SAS Institute Inc.,Cary, N.C., USA).

Experimental Results:

Tables 178-180 summarize the observed phenotypes of transgenic plantsexpressing the genes constructs using the GH-SB Assays.

The genes listed in Tables 178-180 improved plant performance when grownat normal conditions. These genes produced larger plants with a largerphotosynthetic area, biomass (fresh weight, dry weight, rosettediameter, rosette area and plot coverage), relative growth rate, bladerelative area and petiole relative area. The genes were cloned under theregulation of a constitutive At6669 promoter (SEQ ID NO: 15751). Theevaluation of each gene was performed by testing the performance ofdifferent number of events. Event with p-value<0.1 was consideredstatistically significant

TABLE 178 Genes showing improved plant performance at Normal growthconditions under regulation of At6669 promoter Dry Weight [mg] FreshWeight [mg] Leaf Number P- % P- % P- % Gene Name Event # Ave. Val. Incr.Ave. Val. Incr. Ave. Val. Incr. LYD897  84444.13 117.5  0.18 10 — — — —— — LYD888 84613.2 117.5  0.18 10 1481.2  0.09 13 — — — LYD869_H185982.3 116.2  0.27  9 — — — — — — LYD869_H1 85983.1 126.9  0.03 191512.5  0.18 16 — — — LYD859 83953.6 — — — 1431.2  0.29  9 — — — LYD85983957.5 121.9  0.12 14 1525.0  0.25 17 10.4 0.04 9 LYD853 86496.1 118.8 0.18 11 — — — 10.1 0.08 5 LYD853 86497.6 120.0  0.12 13 1475.0  0.09 13— — — LYD853 86497.7 125.0  0.22 17 — — — — — — LYD828 85324.2 118.8 0.15 11 — — — — — — LYD828 85324.4 — — — 1400.0  0.27  7 — — — LYD82685587.2 118.8  0.18 11 1425.0  0.17  9 — — — LYD795 85978.4 — — — — — —10.2 0.02 7 LYD790 84574.2 118.8  0.15 11 1406.2  0.24  8 — — — LYD79084574.5 115.6  0.26  9 — — — — — — LYD756 85069.8 — — — — — — 10.1 0.225 LYD750 84966.3 128.1  0.07 20 1593.8  0.18 22 — — — LYD744 86509.2120.6  0.12 13 1406.2  0.26  8 — — — LYD699 85972.6 126.2  0.07 181481.2  0.17 13 — — — CONT. — 106.6  — — 1307.7  — —  9.61 — — LYD90884445.1 50.0 0.11 21 687.5 0.02 31 10.6 L 11  LYD908 84446.1 — — — — — —10.4 0.01 8 LYD908 84447.1 60.0 L 45 781.2 0.02 49 10.9 L 14  LYD90884447.4 61.9 L 50 781.2 0.12 49 10.7 0.11 11  LYD876 83416.3 51.9 0.2526 706.2 0.05 35 10.6 L 11  LYD876 83417.3 57.5 0.01 39 631.2 0.26 20 —— — LYD876 83417.6 — — — — — — 10.5 L 9 LYD876 83418.2 — — — — — — 10.5L 9 LYD865 83730.1 — — — — — — 11.1 0.07 15  LYD865 83731.1 — — — — — —10.2 0.15 7 LYD865 83733.5 — — — — — — 10.2 0.29 7 LYD864 83406.2 — — —— — — 10.3 0.20 8 LYD864 83406.4 55.6 0.04 35 675.0 0.02 29 — — — LYD86483409.2 — — — — — — 10.8 0.09 13  LYD864 83409.3 56.2 0.02 36 806.2 0.0454 10.6 0.23 10  LYD864 83409.4 — — — — — — 10.3 0.06 8 LYD843 83772.153.1 0.04 29 700.0 0.02 33 10.4 0.12 8 LYD843 83774.1 — — — — — — 10.10.16 5 LYD843 83775.2 56.2 0.24 36 787.5 0.14 50 — — — LYD843 83775.458.8 0.14 42 706.2 0.05 35 10.0 0.11 4 LYD842 83524.4 48.8 0.17 18 618.80.11 18  9.94 0.11 4 LYD842 83526.5 — — — — — — 10.3 L 8 LYD842 83528.251.9 0.06 26 668.8 0.03 27 10.7 0.02 11  LYD835 84139.1 — — — 612.5 0.1317 10.7 0.02 11  LYD835 84141.2 — — — — — — 10.1 0.16 5 LYD835 84141.359.4 L 44 681.2 0.02 30 10.2 0.10 6 LYD835 84143.1 — — — — — — 10.6 0.1310  LYD835 84143.2 55.6 0.02 35 693.8 0.03 32  9.81 0.27 2 LYD82184053.3 62.5 L 52 825.0 L 57 11.9 0.08 24  LYD821 84054.1 65.0 0.17 58775.0 0.03 48 10.9 L 14  LYD821 84054.4 — — — 606.2 0.16 15 10.7 0.0211  LYD821 84054.6 — — — — — — 10.1 0.16 5 LYD793 83499.5 — — — — — — 9.88 0.24 3 LYD793 83499.7 50.0 0.29 21 — — — — — — LYD793 83500.4 57.50.09 39 737.5 L 40 10.7 0.11 11  LYD777 83489.3 — — — 662.5 0.20 26 10.20.03 7 LYD777 83491.3 — — — — — —  9.81 0.27 2 LYD777 83492.3 — — —637.5 0.09 21 10.2 0.15 7 LYD777 83492.4 — — — 637.5 0.07 21 — — —LYD777 83493.3 60.0 L 45 762.5 L 45 — — — LYD767 83485.1 52.5 0.05 27787.5 L 50 10.8 L 12  LYD767 83486.2 49.4 0.15 20 737.5 L 40 10.7 0.1111  LYD767 83488.1 — — — 656.2 0.25 25 10.0 0.11 4 LYD767 83488.5 — — —662.5 0.08 26 10.8 L 12  LYD753 83916.1 — — — 656.2 0.04 25 10.4 L 8LYD753 83917.2 — — — — — — 10.2 0.02 6 LYD753 83917.6 66.9 L 62 806.2 L54 11.5 L 20  LYD735 84165.1 — — — — — — 10.1 0.21 6 LYD735 84168.2 68.80.17 67 — — — 10.5 L 9 LYD730 84258.1 52.5 0.07 27 712.5 0.03 36 11.40.02 19  LYD730 84259.1 — — — 637.5 0.20 21 — — — LYD729 84159.1 — — — —— — 10.7 0.11 11  LYD729 84159.4 — — — — — — 10.6 L 10  LYD729 84159.6 —— — 675.0 0.02 29 10.4 0.01 8 LYD729 84160.3 65.6 0.05 59 831.2 0.13 5810.6 0.13 10  LYD729 84163.2 — — — 612.5 0.22 17 — — — LYD726 84591.165.6 0.05 59 837.5 0.04 60 11.1 0.07 15  LYD726 84593.1 65.0 0.04 58843.8 L 61 11.2 L 17  LYD726 84595.1 — — — 718.8 0.04 37 — — — LYD72684595.3 — — — — — — 10.7 L 11  LYD720 83761.3 — — — — — — 10.1 0.05 6LYD720 83763.1 75.3 L 82 1035.7  0.30 97 10.8 L 13  LYD720 83764.2 — — —737.5 0.23 40 10.4 0.04 9 LYD720 83764.3 — — — 718.8 L 37 10.8 0.02 13 LYD705 83382.6 — — — — — — 10.2 0.03 7 LYD705 83384.4 — — — 687.5 0.0231 — — — CONT. — 41.2 — — 525.0 — —  9.59 — — LGP8 75405.1 — — — — — —12.5 0.10 6 LGP20 76945.5 — — — 4365.6  0.14 10 — — — CONT. — — — —3975.9  — — 11.8 — — LGP43 76955.2 — — — 5075.0  0.07  6 — — — CONT. — —— — 4801.8  — — — — — LYD914 84179.2 55.6 0.22 13 631.2 0.22 23 — — —LYD914 84183.6 53.1 0.10  8 — — — 11.9 0.10 4 LYD901 83883.3 — — — — — —12.1 0.16 6 LYD892 84250.5 55.6 0.02 13 — — — — — — LYD892 84250.7 61.90.01 26 718.8 L 40 — — — LYD876 83418.2 — — — — — — 11.8 0.07 3 LYD87683418.3 — — — 642.0 0.05 25 — — — LYD870 83815.7 — — — 591.1 0.23 15 — —— LYD864 83409.3 — — — — — — 11.8 0.21 2 LYD864 83409.4 — — — — — — 12.5L 9 LYD847 83403.1 — — — 601.8 0.14 17 — — — LYD843 83772.1 55.0 0.05 12— — — — — — LYD843 83775.2 57.5 0.09 17 — — — — — — LYD842 83526.5 — — —668.8 0.26 30 — — — LYD781 83496.3 53.2 0.20  8 — — — — — — LYD75584033.1 — — — 593.8 0.20 16 11.8 0.26 3 LYD753 83917.6 — — — — — — 11.90.16 4 LYD735 84165.1 — — — 612.5 0.07 19 — — — LYD727 83791.1 — — —613.4 0.07 20 — — — LYD727 83793.2 — — — — — — 11.8 0.26 3 LYD72783795.2 — — — 656.2 0.02 28 — — — LYD722 84944.3 59.4 0.21 21 — — — 12.00.05 5 LYD722 84944.4 57.5 0.21 17 656.2 0.02 28 12.4 0.15 8 CONT. —49.1 — — 513.3 — — 11.5 — — LGP1 76249.3 — — — — — — 11.7 0.25 3 LGP176250.4 — — — — — — 11.7 0.24 4 CONT. — — — — — — — 11.3 — — LYD92283821.3 60.0 0.06 25 868.8 0.02 38 — — — LYD922 83823.5 65.0 0.04 35 — —— 10.9 0.15 5 LYD922 83823.6 — — — — — — 11.0 0.08 6 LYD905 84147.2 — —— — — — 11.1 0.05 7 LYD901 83883.2 64.6 0.25 34 736.6 0.26 17 11.2 0.068 LYD901 83883.3 — — — — — — 11.0 0.17 6 LYD901 83886.6 61.9 0.03 29812.5 0.04 29 11.4 0.01 10  LYD883 83911.3 56.9 0.17 18 737.5 0.21 17 —— — LYD883 83912.2 57.5 0.09 20 775.0 0.14 23 11.3 0.11 9 LYD883 83912.358.1 0.08 21 837.5 0.02 33 11.6 0.23 11  LYD860 83622.1 54.4 0.23 13 — —— — — — LYD860 83625.4 — — — 812.5 0.12 29 12.2 0.24 17  LYD839 83521.3— — — — — — 10.8 0.27 4 LYD839 83522.1 58.1 0.13 21 — — — — — — LYD83983523.1 — — — — — — 10.9 0.15 5 LYD839 83523.6 — — — 762.5 0.10 21 — — —LYD836 83514.4 — — — — — — 11.6 0.18 12  LYD836 83515.5 — — — 756.2 0.1220 — — — LYD833 83512.2 — — — 731.2 0.19 16 — — — LYD833 83513.5 55.60.18 16 775.0 0.08 23 11.4 L 10  LYD811 83713.4 — — — 737.5 0.21 17 — —— LYD789 84130.3 57.5 0.26 20 775.0 0.30 23 — — — LYD789 84131.3 — — —718.8 0.27 14 — — — LYD781 83494.1 58.1 0.09 21 — — — — — — LYD78183494.4 54.4 0.23 13 — — — 10.8 0.23 4 LYD755 84032.1 56.9 0.12 18 756.20.27 20 10.8 0.25 4 LYD755 84035.1 — — — 800.0 0.05 27 — — — LYD75584035.2 59.4 0.06 24 — — — 12.1 L 16  LYD742 83467.4 — — — 756.2 0.22 2010.8 0.18 4 LYD739 83386.2 58.1 0.19 21 — — — 11.7 L 13  LYD739 83389.4— — — 725.0 0.22 15 — — — LYD725 84190.3 — — — 856.2 0.02 36 11.3 0.02 9LYD725 84191.1 61.2 0.08 28 856.2 0.02 36 — — — LYD704 83781.1 60.6 0.0426 — — — — — — LYD704 83785.7 — — — — — — 10.8 0.25 4 CONT. — 48.0 — —628.8 — — 10.4 — — LYD925 85844.1 71.0 0.13 27 919.6 L 34 11.4 L 11 LYD925 85844.3 70.6 0.06 26 750.0 0.28 10 — — — LYD920 83760.3 63.1 0.2813 768.8 0.15 12 10.9 0.20 5 LYD897 84444.6 — — — — — — 11.7 0.13 13 LYD869_H1 85983.1 75.6 0.27 35 — — — 10.9 0.20 5 LYD854 84992.3 70.60.10 26 — — — 11.0 0.27 7 LYD854 84993.2 68.1 0.08 21 — — — — — — LYD82685585.1 — — — — — — 10.7 0.19 4 LYD826 85587.1 68.8 0.07 23 850.0 0.1524 11.7 L 13  LYD826 85587.5 67.5 0.27 20 — — — — — — LYD824 83903.376.9 0.01 37 993.8 L 45 — — — LYD824 83905.3 76.2 0.24 36 1000.0  0.0246 10.7 0.19 4 LYD824 83907.2 — — — — — — 10.9 0.06 5 LYD824 83907.6 — —— — — — 11.6 0.07 12  LYD816 85591.1 75.6 0.01 35 1025.0  L 50 — — —LYD816 85594.2 — — — — — — 11.5 0.28 11  LYD814 84971.2 — — — — — — 10.70.19 4 LYD814 84973.3 — — — — — — 10.8 0.11 5 LYD814 84973.6 75.0 0.0234 — — — 11.4 0.05 10  LYD791 85129.4 81.2 0.01 45 925.0 L 35 11.8 L 14 LYD791 85129.5 74.2 0.03 32 933.9 L 37 11.1 0.02 7 LYD790 84574.2 88.8 L58 1100.0  L 61 11.9 0.10 16  LYD778 85053.2 — — — — — — 11.0 0.04 7LYD778 85053.3 62.6 0.30 12 817.9 0.24 20 11.2 0.01 9 LYD774 83938.1 — —— — — — 10.8 0.16 4 LYD774 83938.4 65.0 0.19 16 — — — — — — LYD77483940.2 70.6 0.05 26 868.8 0.05 27 11.2 L 9 LYD769 84121.5 77.5 0.09 38— — — 11.0 0.14 7 LYD769 84123.1 73.3 0.27 31 851.8 0.21 25 11.2 0.01 9LYD769 84123.3 — — — — — — 11.2 0.01 9 LYD756 85067.2 — — — 881.2 0.2829 11.1 0.02 8 LYD756 85069.8 69.4 0.24 24 — — — 10.9 0.10 6 LYD75285046.5 — — — 743.8 0.29  9 — — — LYD752 85047.2 — — — — — — 10.7 0.19 4LYD752 85049.1 77.5 L 38 887.5 0.10 30 11.1 0.02 8 LYD741 84426.6 67.10.25 20 — — — — — — LYD741 84426.7 — — — — — — 10.8 0.17 5 LYD70284412.3 — — — — — — 10.7 0.29 4 CONT. — 56.1 — — 683.9 — — 10.3 — —LYD917 84186.4 — — — — — — 11.8 L 8 LYD917 84187.1 57.0 0.19 22 — — — —— — LYD917 84188.2 53.1 0.21 14 — — — — — — LYD917 84188.3 53.2 0.09 14— — — — — — LYD912 83820.5 — — — — — — 11.4 0.14 5 LYD908 84447.4 58.30.23 25 — — — 11.4 0.14 5 LYD905 84145.4 52.5 0.19 13 — — — — — — LYD90584146.3 56.9 0.09 22 662.5 0.01 33 — — — LYD905 84147.2 54.4 0.03 17 — —— 11.9 0.02 9 LYD905 84147.5 — — — — — — 11.4 0.12 4 LYD860 83625.4 50.50.29  9 — — — 11.2 0.29 3 LYD838 83997.2 — — — — — — 11.4 0.26 4 LYD83883998.1 — — — — — — 11.4 0.26 4 LYD838 83999.2 — — — — — — 11.2 0.29 3LYD838 84000.2 52.1 0.17 12 566.1 0.19 14 11.6 0.03 6 LYD836 83516.2 — —— — — — 11.2 0.24 3 LYD836 83518.2 — — — 568.8 0.25 14 — — — LYD83584141.2 — — — — — — 11.2 0.24 3 LYD835 84141.3 — — — — — — 11.3 0.14 4LYD809 83504.4 — — — — — — 11.4 0.07 5 LYD767 83485.1 — — — 681.2 L 37 —— — LYD767 83488.1 — — — 562.5 0.26 13 — — — LYD767 83488.5 58.1 0.16 25— — — 11.4 0.29 5 LYD742 83467.4 63.9 0.28 37 — — — — — — LYD738 84027.1— — — 600.0 0.15 20 11.5 0.18 5 LYD729 84159.4 — — — 573.2 0.15 15 — — —LYD729 84161.2 54.8 0.08 18 — — — 11.4 0.12 4 LYD726 84593.1 51.9 0.1112 — — — — — — LYD726 84595.3 — — — — — — 11.8 L 8 LYD725 84189.3 55.00.03 18 — — — — — — LYD705 83382.6 56.9 0.19 22 — — — — — — CONT. — 46.5— — 498.7 — — 10.9 — — LYD874 84407.1 — — — 721.4 0.11 10 — — — LYD87485656.1 55.0 0.04 13 700.0 0.24  7 10.6 0.11 8 LYD874 85658.1 56.9 0.0517 750.0 0.25 15 — — — LYD834 84452.4 54.4 0.13 12 — — — 10.8 0.18 9LYD829 85058.4 59.4 L 22 787.5 L 20 10.9 0.01 10  LYD829 85058.8 — — —752.7 0.03 15 10.7 0.02 8 LYD829 85059.3 51.9 0.25  6 — — — — — — LYD80685557.1 68.8 L 41 906.2 L 39 11.6 L 18  LYD798 84533.1 — — — 731.2 0.1712 10.2 0.27 3 LYD798 84533.4 61.9 0.06 27 731.2 0.17 12 — — — LYD79884533.5 53.1 0.21  9 — — — — — — LYD794 86031.4 — — — 706.2 0.23  8 — —— LYD765 85811.2 58.8 0.25 21 768.8 0.15 18 10.8 0.21 10  LYD765 85811.3— — — 751.8 0.06 15 — — — LYD765 85814.2 66.2 L 36 825.0 0.16 26 — — —LYD762 85112.5 66.9 0.25 37 837.5 0.29 28 11.3 0.04 15  LYD762 85112.7 —— — — — — 10.6 0.11 8 LYD762 85114.3 60.6 0.01 24 781.2 0.12 20 10.80.18 9 LYD761 83477.2 54.4 0.06 12 — — — — — — LYD760 83699.1 58.0 L 19— — — 10.2 0.27 3 LYD760 83703.2 57.5 0.08 18 — — — 10.6 0.11 8 LYD75485597.1 56.2 0.11 15 737.5 0.30 13 — — — LYD754 85597.2 57.5 0.02 18737.5 0.06 13 10.4 0.08 6 LYD754 85598.1 — — — — — — 10.6 0.19 7 LYD75185720.2 59.4 0.02 22 768.8 0.23 18 — — — LYD751 85720.3 — — — — — — 10.60.23 8 LYD749 84423.6 — — — — — — 10.3 0.22 4 LYD749 84423.8 — — — — — —10.5 0.29 7 LYD711 85315.1 — — — — — — 10.9 0.01 10  LYD711 85316.3 55.60.20 14 725.0 0.09 11 — — — LYD711 85316.5 70.6 L 45 868.8 L 33 11.2 L14  LYD703 85102.2 — — — — — — 10.2 0.27 3 CONT. — 48.8 — — 653.6 — — 9.86 — — LYD925 85840.1 — — — — — —  9.69 0.10 8 LYD925 85844.1 112.5 0.11 12 1387.5  0.16 11  9.50 L 6 LYD924 86506.3 112.5  0.11 12 — — — —— — LYD924 86506.5 111.9  0.29 12 1362.5  0.24  9  9.69 L 8 LYD88484576.1 128.1  0.17 28 — — —  9.31 0.05 3 LYD884 84579.2 — — — — — — 9.56 L 6 LYD884 84580.3 — — — — — —  9.62 0.03 7 LYD879 85963.1 127.5 0.02 27 1556.2  0.20 24  9.44 0.19 5 LYD879 85964.1 — — — — — —  9.250.24 3 LYD878 84487.1 110.6  0.16 11 1393.8  0.11 11  9.50 0.06 6 LYD878 84488.11 — — — — — —  9.19 0.21 2 LYD878 84488.5 113.1  0.15 13 1362.5 0.20  9 — — — LYD878 84488.8 111.9  0.29 12 1475.0  0.24 18 — — — LYD83484452.3 — — — — — —  9.62 0.19 7 LYD834 84452.4 — — — 1343.8  0.28  7 —— — LYD829 85058.3 120.6  0.02 21 1531.2  0.22 22 — — — LYD829 85058.4108.8  0.22  9 — — —  9.50 0.06 6 LYD829 85058.8 122.5  0.16 22 1450.0 0.11 16  9.50 L 6 LYD829 85059.2 — — — 1481.2  0.29 18 — — — LYD82985059.3 108.8  0.22  9 1375.0  0.17 10  9.56 L 6 LYD813 83725.1 115.6 0.25 16 1493.8  0.15 19 — — — LYD813 83725.2 112.5  0.19 12 1443.8  0.1015  9.75 0.15 8 LYD813 83726.5 — — — — — —  9.31 0.30 3 LYD813 83728.1 —— — 1356.2  0.22  8 — — — LYD804 84134.1 121.9  0.02 22 1568.8  L 25 — —— LYD804 84134.2 110.6  0.28 11 — — —  9.56 0.13 6 LYD804 84137.5 — — —— — —  9.25 0.08 3 LYD804 84138.2 113.8  0.08 14 — — — — — — LYD80484138.5 — — — — — —  9.38 0.02 4 LYD798 84533.1 — — — — — —  9.62 L 7LYD798 84533.3 — — — — — —  9.94 0.26 10  LYD798 84533.6 — — — 1437.5 0.06 15 10.0 L 11  LYD784 84605.1 113.8  0.15 14 1393.8  0.12 11 — — —LYD784 86519.3 — — — — — — 10.1 0.18 12  LYD780 86514.1 — — — — — — 9.44 0.01 5 LYD780 86514.2 121.2  0.26 21 1531.2  0.15 22  9.69 0.10 8LYD757 83470.2 — — — — — —  9.56 0.30 6 LYD757 83470.5 — — — 1450.0 0.24 16  9.69 0.24 8 LYD757 83472.1 110.0  0.28 10 1400.0  0.10 12 — — —LYD757 83473.4 — — — — — —  9.62 0.03 7 LYD754 85597.1 124.4  0.08 241587.5  0.19 27 10.0 L 11  LYD754 85597.2 125.0  0.06 25 1568.8  0.02 25— — — LYD754 85599.4 — — — — — —  9.50 0.06 6 LYD751 85720.3 118.1  0.0618 1587.5  L 27  9.75 0.15 8 LYD751 85722.1 127.5  0.04 27 1606.2  L 28 9.69 0.10 8 LYD751 85722.2 114.4  0.07 14 1443.8  0.07 15  9.75 0.15 8LYD751 85724.1 — — — — — —  9.88 0.01 10  LYD722 84941.2 113.8  0.11 141387.5  0.19 11  9.25 0.24 3 LYD722 84944.3 — — — — — —  9.31 0.30 3LYD722 84945.1 — — — — — — 10.2 L 13  LYD714 84071.1 109.1  0.25  91397.3  0.14 12 — — — LYD714 84074.2 123.8  0.01 24 1412.5  0.13 13 — —— LYD714 84075.1 — — — — — —  9.44 0.01 5 LYD714 84075.4 — — — — — — 9.50 0.06 6 LYD702 84411.6 — — — — — —  9.19 0.21 2 LYD702 84411.8 — —— 1343.8  0.28  7 — — — LYD702 84412.3 121.9  0.01 22 1493.8  0.05 1910.1 0.15 12  LYD702 84412.6 115.0  0.06 15 1362.5  0.24  9 — — — CONT.— 100.1  — — 1252.4  — —  9.00 — — LGP49 77651.3 — — — — — — 12.0 0.16 6LGP49 77651.8 — — — — — — 12.0 0.07 6 LGP49 77652.6 — — — — — — 11.80.26 3 CONT. — — — — — — — 11.4 — — LGP44 75764.8 — — — — — — 11.8 0.124 LGP44 75765.3 — — — 5093.8  0.11  5 — — — CONT. — — — — 4866.7  — —11.3 — — LGP8 75409.5 278.7  0.08  6 4003.6  0.07 11 11.9 0.02 8 LGP2176332.1 286.3  0.18  9 3945.0  0.27  9 — — — LGP20 76941.5 — — — — — —12.0 0.01 9 CONT. — 262.8  — — 3606.2  — — 11.0 — — LYD849 86622.2 — — —— — — 10.1 0.35 5 LYD841 85885.2 — — — 1381.2  0.43  6 — — — LYD83086932.6 113.1  0.41  6 — — — — — — CONT. — 106.6  — — 1307.7  — —  9.61— — LYD926 83826.2 — — — — — — 10.2 0.48 4 LYD926 83830.2 — — — — — —10.4 0.48 6 LYD926 83830.3 58.6 0.45 20 — — — — — — CONT. — 48.8 — — — ——  9.86 — — LYD803 87331.3 — — — — — —  9.88 0.06 5 CONT. — — — — — — — 9.38 — — Table 178. “CONT.”—Control; “Ave.”—Average; “% Incr.” = %increment; “p-val.”—p-value, L- p < 0.01.

TABLE 179 Genes showing improved plant performance at Normal growthconditions under regulation of At6669 promoter Rosette Diameter PlotCoverage [cm²] Rosette Area [cm²] [cm] P- % P- % P- % Gene Name Event #Ave. Val. Incr. Ave. Val. Incr. Ave. Val. Incr. LYD888 84614.1 60.4 0.21 7  7.56 0.21  7 — — — LYD869_H1 85983.1 73.8 0.01 31  9.23 0.01 31 5.13L 14  LYD859 83953.3 61.5 0.10  9  7.69 0.10  9 4.78 0.03 6 LYD85983957.5 68.7 0.20 22  8.58 0.20 22 5.00 0.23 11  LYD853 86496.1 66.00.01 17  8.25 0.01 17 4.87 0.04 8 LYD853 86497.7 69.3 0.15 23  8.66 0.1523 4.95 L 10  LYD828 85324.4 61.9 0.08 10  7.74 0.08 10 4.70 0.09 4LYD826 85587.1 62.2 0.24 11  7.78 0.24 11 4.70 0.13 4 LYD826 85587.267.2 0.03 20  8.40 0.03 20 4.85 0.01 8 LYD795 85978.4 62.7 0.18 11  7.840.18 11 4.81 0.27 7 LYD790 84574.2 61.6 0.27 10  7.71 0.27 10 — — —LYD750 84966.3 — — — — — — 4.92 0.27 9 LYD744 86509.2 — — — — — — 4.640.21 3 LYD744 86509.4 — — — — — — 4.86 0.18 8 LYD699 85972.6 64.4 0.0215  8.05 0.02 15 4.73 0.06 5 CONT. — 56.2 — —  7.03 — — 4.50 — — LYD90884445.1 79.1 L 31  9.89 L 31 5.34 0.15 13  LYD908 84446.1 73.5 0.02 22 9.18 0.02 22 5.08 0.10 7 LYD908 84447.1 89.9 L 49 11.2 L 49 5.56 L 17 LYD908 84447.4 88.3 L 47 11.0 L 47 5.70 0.01 20  LYD876 83416.3 82.00.06 36 10.2 0.06 36 5.28 0.03 11  LYD876 83417.3 75.8 L 26  9.48 L 265.11 0.06 8 LYD876 83418.2 72.0 0.24 20  9.00 0.24 20 — — — LYD86583730.1 79.4 0.21 32  9.92 0.21 32 5.29 0.23 12  LYD865 83733.5 82.10.25 36 10.3 0.25 36 — — — LYD864 83406.4 72.1 0.03 20  9.02 0.03 205.09 0.17 7 LYD864 83409.3 90.2 0.05 50 11.3 0.05 50 5.62 0.01 19 LYD843 83772.1 79.4 L 32  9.93 L 32 5.37 0.06 13  LYD843 83774.1 74.40.27 24  9.30 0.27 24 — — — LYD843 83775.2 88.9 0.15 48 11.1 0.15 485.64 0.09 19  LYD843 83775.4 77.7 0.07 29  9.71 0.07 29 5.22 0.18 10 LYD842 83524.4 70.0 0.17 16  8.75 0.17 16 5.03 0.17 6 LYD842 83528.274.0 0.03 23  9.26 0.03 23 5.13 0.07 8 LYD835 84139.1 75.2 0.01 25  9.400.01 25 5.23 0.02 10  LYD835 84141.3 73.7 0.03 23  9.22 0.03 23 5.160.04 9 LYD835 84143.1 69.7 0.19 16  8.71 0.19 16 — — — LYD835 84143.280.2 L 33 10.0 L 33 5.29 0.01 11  LYD821 84053.3 92.5 L 54 11.6 L 545.67 L 20  LYD821 84054.1 83.7 L 39 10.5 L 39 5.40 L 14  LYD821 84054.471.8 0.03 19  8.97 0.03 19 5.16 0.04 9 LYD793 83499.7 81.1 0.29 35 10.10.29 35 5.32 0.26 12  LYD793 83500.4 79.2 0.02 32  9.90 0.02 32 5.290.01 11  LYD777 83489.3 74.8 0.12 24  9.35 0.12 24 5.08 0.28 7 LYD77783492.3 74.1 0.01 23  9.26 0.01 23 5.17 0.03 9 LYD777 83492.4 71.3 0.0418  8.91 0.04 18 5.18 0.03 9 LYD777 83493.3 81.4 L 35 10.2 L 35 5.34 L13  LYD767 83485.1 85.4 L 42 10.7 L 42 5.50 0.04 16  LYD767 83486.2 79.6L 32  9.95 L 32 5.26 0.02 11  LYD767 83488.1 73.6 0.06 22  9.20 0.06 225.12 0.18 8 LYD767 83488.5 73.8 0.02 23  9.23 0.02 23 5.15 0.04 9 LYD75383916.1 77.1 L 28  9.64 L 28 5.31 0.01 12  LYD753 83917.6 92.4 L 54 11.5L 54 5.66 L 19  LYD735 84167.1 68.7 0.25 14  8.59 0.25 14 — — — LYD73584168.2 78.6 L 31  9.82 L 31 5.31 0.01 12  LYD730 84258.1 80.7 L 34 10.1L 34 5.32 0.07 12  LYD729 84159.1 — — — — — — 5.40 0.25 14  LYD72984159.4 76.2 0.01 27  9.52 0.01 27 5.08 0.15 7 LYD729 84159.6 77.9 L 29 9.73 L 29 5.22 0.02 10  LYD729 84160.3 80.6 L 34 10.1 L 34 5.25 0.0411  LYD729 84163.2 71.6 0.12 19  8.94 0.12 19 5.15 0.17 8 LYD726 84591.192.8 L 54 11.6 L 54 5.63 0.03 19  LYD726 84593.1 90.6 L 51 11.3 L 515.71 L 20  LYD726 84595.1 80.0 0.18 33  10.00 0.18 33 5.38 0.05 13 LYD720 83761.2 71.8 0.19 19  8.98 0.19 19 5.06 0.25 7 LYD720 83761.366.4 0.19 10  8.30 0.19 10 4.95 0.24 4 LYD720 83763.1 88.4 0.04 47 11.00.04 47 5.57 L 17  LYD720 83764.2 81.5 0.11 35 10.2 0.11 35 5.34 0.1213  LYD720 83764.3 78.9 0.01 31  9.86 0.01 31 5.30 0.05 12  LYD70583380.2 65.0 0.28  8  8.13 0.28  8 — — — LYD705 83384.4 71.3 0.04 19 8.91 0.04 19 5.11 0.06 8 CONT. — 60.2 — —  7.52 — — 4.74 — — LGP875405.1 83.7 0.27  8 10.5 0.27  8 5.33 0.26 5 CONT. — 77.7 — —  9.71 — —5.09 — — LGP43 76955.2 77.8 0.24  6  9.73 0.24  6 5.26 0.17 4 CONT. —73.2 — —  9.15 — — 5.06 — — LYD914 84179.2 120.1  0.03 28 15.0 0.03 286.58 0.14 14  LYD914 84179.4 101.4  0.22  8 12.7 0.22  8 — — — LYD91484183.6 121.1  L 29 15.1 L 29 6.73 L 16  LYD892 84250.7 130.4  0.15 3916.3 0.15 39 6.63 0.07 15  LYD876 83418.3 113.1  0.15 20 15.1 L 28 6.66L 15  LYD864 83409.3 102.8  0.25  9 12.8 0.25  9 6.07 0.08 5 LYD86483409.4 120.0  L 28 15.0 L 28 6.52 L 13  LYD843 83774.1 106.9  0.08 1413.4 0.08 14 6.17 0.02 7 LYD842 83526.5 113.0  0.01 20 14.1 0.01 20 6.44L 11  LYD781 83498.3 104.4  0.21 11 13.1 0.21 11 6.18 0.06 7 LYD75584035.2 — — — — — — 5.98 0.22 3 LYD753 83917.2 120.5  0.20 28 15.1 0.2028 6.63 0.26 15  LYD735 84165.1 113.5  0.03 21 14.2 0.03 21 6.28 0.14 9LYD727 83791.1 109.7  0.03 17 13.7 0.03 17 6.36 0.06 10  LYD727 83795.2119.1  0.07 27 14.9 0.07 27 6.51 0.02 13  LYD722 84944.3 116.2  0.27 2414.5 0.27 24 — — — LYD722 84944.4 123.9  L 32 15.5 L 32 6.57 L 13 LYD720 83763.1 109.8  0.07 17 13.7 0.07 17 6.35 L 10  CONT. — 94.0 — —11.7 — — 5.79 — — LYD922 83821.3 97.5 0.21 23 12.2 0.21 23 5.91 0.03 11 LYD922 83823.6 94.3 0.03 19 11.8 0.03 19 5.81 0.01 9 LYD901 83883.2 91.10.13 15 11.5 0.07 16 5.74 0.02 8 LYD901 83886.6 93.9 0.04 19 11.7 0.0419 5.72 0.09 8 LYD883 83911.3 — — — — — — 5.47 0.29 3 LYD883 83912.291.2 0.05 15 11.4 0.05 15 5.70 0.05 7 LYD883 83912.3 103.9  L 31 13.0 L31 6.03 0.01 14  LYD860 83625.4 93.8 0.05 19 11.7 0.05 19 5.81 0.09 9LYD836 83514.4 99.3 0.30 26 12.4 0.30 26 5.88 0.24 11  LYD836 83515.588.7 0.23 12 11.1 0.23 12 5.55 0.28 5 LYD833 83512.2 86.9 0.16 10 10.90.16 10 5.56 0.12 5 LYD833 83513.5 94.1 0.03 19 11.8 0.03 19 5.79 0.01 9LYD811 83713.4 — — — — — — 5.53 0.18 4 LYD755 84032.1 87.0 0.18 10 10.90.18 10 5.49 0.28 3 LYD755 84035.1 97.0 0.01 23 12.1 0.01 23 5.80 0.01 9LYD755 84035.2 93.6 0.14 18 11.7 0.14 18 5.67 0.09 7 LYD742 83467.3 — —— — — — 5.56 0.27 5 LYD725 84190.3 96.3 0.03 22 12.0 0.03 22 5.83 0.0210  LYD725 84191.1 94.6 0.02 20 11.8 0.02 20 5.70 0.23 7 LYD725 84191.285.9 0.29  9 10.7 0.29  9 5.68 0.25 7 CONT. — 79.1 — —  9.89 — — 5.31 —— LYD925 85844.1 104.1  0.09 30 13.0 0.09 30 6.17 0.18 14  LYD92585844.3 89.2 0.21 11 11.2 0.21 11 5.74 0.16 6 LYD920 83760.3 88.3 0.1910 11.0 0.19 10 5.65 0.28 4 LYD869_H1 85982.5 88.2 0.18 10 11.0 0.18 105.95 0.04 10  LYD869_H1 85983.1 101.4  0.19 27 12.7 0.19 27 6.17 0.1014  LYD854 84993.2 91.0 0.09 14 11.4 0.09 14 5.90 0.08 9 LYD826 85587.199.6 0.08 24 12.5 0.08 24 6.08 0.02 12  LYD826 85587.5 91.4 0.15 14 11.40.15 14 — — — LYD824 83903.3 107.2  0.10 34 13.4 0.10 34 6.50 0.15 20 LYD824 83905.3 106.6  L 33 13.3 L 33 6.33 0.04 17  LYD824 83907.2 94.50.06 18 11.8 0.06 18 5.83 0.08 8 LYD824 83907.6 89.3 0.16 12 11.2 0.1612 — — — LYD816 85591.1 118.1  L 47 14.8 L 47 6.89 0.04 27  LYD81685594.2 93.1 0.16 16 11.6 0.16 16 5.90 0.13 9 LYD791 85129.4 103.3  0.0729 12.9 0.07 29 6.10 0.19 13  LYD791 85129.5 100.0  L 25 13.4 0.06 346.45 0.02 19  LYD790 84574.2 124.0  L 55 15.5 L 55 6.83 L 26  LYD77885053.3 93.6 0.05 17 11.7 0.05 17 5.87 0.07 8 LYD774 83938.4 96.8 0.0421 12.1 0.04 21 5.96 0.07 10  LYD774 83940.2 102.3  L 28 12.8 L 28 6.040.02 12  LYD769 84121.5 — — — — — — 6.28 0.23 16  LYD769 84123.1 106.0 L 32 13.2 L 32 6.12 0.08 13  LYD769 84123.3 106.1  0.06 32 13.3 0.06 326.19 0.17 14  LYD756 85067.2 95.5 0.10 19 11.9 0.10 19 — — — LYD75685069.8 94.8 0.27 18 11.9 0.27 18 — — — LYD752 85046.5 — — — — — — 5.710.23 5 LYD752 85049.1 102.7  0.16 28 12.8 0.16 28 6.19 0.24 14  CONT. —80.0 — — 10.0 — — 5.41 — — LYD905 84146.3 112.0  0.18 14 14.0 0.18 146.15 0.25 3 LYD838 83997.1 — — — — — — 6.12 0.28 3 LYD835 84141.3 — — —— — — 6.34 0.23 6 LYD767 83485.1 110.1  0.08 12 13.8 0.08 12 6.20 0.14 4LYD767 83488.1 111.0  0.06 13 13.9 0.06 13 6.43 0.05 8 LYD726 84593.1 —— — — — — 6.22 0.24 4 LYD725 84189.3 107.3  0.16  9 13.4 0.16  9 — — —CONT. — 98.5 — — 12.3 — — 5.95 — — LYD874 85658.1 83.5 0.29  8 10.4 0.29 8 — — — LYD834 84452.4 — — — — — — 5.65 0.29 6 LYD829 85058.4 87.6 0.1313 11.0 0.13 13 5.62 0.22 5 LYD829 85058.8 86.8 0.21 12 10.8 0.21 12 — —— LYD806 85557.1 111.4  0.05 44 13.9 0.05 44 6.35 L 19  LYD806  85557.1784.7 0.26 10 10.6 0.26 10 5.69 0.25 7 LYD798 84533.1 89.8 0.07 16 11.20.07 16 5.66 0.15 6 LYD798 84533.4 98.6 0.01 28 12.3 0.01 28 6.08 0.1814  LYD765 85811.2 89.0 0.24 15 11.1 0.24 15 5.71 0.12 7 LYD762 85112.596.9 0.01 25 12.1 0.01 25 6.02 0.01 13  LYD762 85114.3 102.8  0.05 3312.8 0.05 33 6.29 L 18  LYD754 85597.1 87.0 0.12 13 10.9 0.12 13 — — —LYD754 85597.2 98.0 L 27 12.2 L 27 5.99 0.02 12  LYD749 84423.6 — — — —— — 5.86 0.15 10  LYD711 85315.1 89.3 0.23 16 11.2 0.23 16 5.71 0.11 7LYD711 85316.5 106.0  0.22 37 13.3 0.22 37 6.21 0.20 16  CONT. — 77.3 ——  9.66 — — 5.34 — — LYD925 85840.1 54.6 0.04 13  6.83 0.04 13 4.43 L 7LYD925 85844.1 57.6 0.01 19  7.20 0.01 19 4.67 L 13  LYD924 86506.1 — —— — — — 4.27 0.26 3 LYD924 86506.5 54.3 0.07 12  6.79 0.07 12 4.44 0.118 LYD924 86507.1 60.7 0.08 26  7.59 0.08 26 4.82 L 17  LYD884 84576.154.2 0.04 12  6.77 0.04 12 4.45 L 8 LYD884 84579.2 — — — — — — 4.46 0.058 LYD879 85963.1 63.3 0.21 31  7.91 0.21 31 4.60 0.23 11  LYD879 85964.1— — — — — — 4.32 0.18 5 LYD878 84487.1 53.6 0.11 11  6.70 0.11 11 — — —LYD878 84488.5 57.4 L 19  7.17 L 19 4.57 0.10 11  LYD878 84488.8 57.50.28 19  7.19 0.28 19 — — — LYD834 84452.3 60.6 L 26  7.58 L 26 4.75 L15  LYD834 84452.4 57.4 0.18 19  7.17 0.18 19 4.57 0.28 11  LYD82985058.3 62.2 0.23 29  7.77 0.23 29 — — — LYD829 85058.4 54.0 0.05 12 6.75 0.05 12 4.28 0.12 4 LYD829 85059.2 63.1 L 31  7.89 L 31 4.77 L 15 LYD829 85059.3 55.5 0.01 15  6.94 0.01 15 4.41 0.01 7 LYD813 83725.157.3 0.09 19  7.17 0.09 19 4.54 0.12 10  LYD813 83725.2 56.8 0.06 18 7.10 0.06 18 4.41 0.08 7 LYD813 83726.4 52.6 0.22  9  6.58 0.22  9 — —— LYD804 84134.1 62.3 0.04 29  7.79 0.04 29 4.59 0.12 11  LYD798 84533.153.4 0.05 10  6.67 0.05 10 4.36 0.05 6 LYD798 84533.3 57.2 L 18  7.15 L18 4.49 0.02 9 LYD798 84533.5 — — — — — — 4.31 0.23 4 LYD798 84533.658.7 L 21  7.33 L 21 4.48 L 8 LYD784 84605.1 52.1 0.13  8  6.52 0.13  84.34 0.05 5 LYD780 86514.2 59.8 0.24 24  7.48 0.24 24 — — — LYD75783470.5 59.5 0.27 23  7.43 0.27 23 4.67 0.11 13  LYD757 83472.1 52.20.12  8  6.53 0.12  8 4.45 L 8 LYD757 83473.4 59.2 L 23  7.40 L 23 4.400.02 7 LYD754 85597.1 67.7 0.16 40  8.46 0.16 40 4.93 0.11 19  LYD75485597.2 60.3 L 25  7.54 L 25 4.59 L 11  LYD754 85598.1 51.5 0.17  7 6.44 0.17  7 4.40 0.09 7 LYD751 85720.2 — — —  6.53 0.11  8 4.45 0.21 8LYD751 85720.3 63.7 0.07 32  7.96 0.07 32 4.69 0.01 13  LYD751 85722.158.1 L 20  7.27 L 20 4.46 L 8 LYD751 85722.2 56.6 0.07 17  7.08 0.07 174.39 0.19 6 LYD751 85724.1 53.2 0.05 10  6.66 0.05 10 — — — LYD72284941.1 53.8 0.16 11  6.73 0.16 11 4.36 0.18 6 LYD722 84941.2 57.8 0.1920  7.23 0.19 20 4.43 0.09 7 LYD722 84945.1 53.9 0.04 12  6.73 0.04 124.35 0.04 5 LYD714 84071.1 54.0 0.03 12  6.75 0.03 12 4.45 0.08 8 LYD71484074.2 53.9 0.23 12  6.74 0.23 12 — — — LYD702 84412.2 52.2 0.15  8 6.53 0.15  8 4.34 0.04 5 LYD702 84412.3 60.6 0.10 25  7.57 0.10 25 4.490.11 9 LYD702 84412.6 55.2 0.02 14  6.90 0.02 14 4.38 0.02 6 CONT. —48.3 — —  6.04 — — 4.13 — — LGP49 77652.6 80.4 0.09 16 10.0 0.09 16 5.170.27 5 CONT. — 69.2 — —  8.65 — — 4.94 — — LGP25 75389.4 — — — — — —5.72 0.12 5 LGP25 75390.4 92.5 0.28  5 11.6 0.28  5 5.67 0.10 4 CONT. —88.4 — — 11.1 — — 5.43 — — LGP44 75764.8 68.2 0.06  9  8.53 0.06  9 4.750.06 3 LGP10 75385.3 68.6 0.29  9  8.57 0.29  9 4.81 0.21 5 CONT. — 62.8— —  7.85 — — 4.60 — — LGP20 76941.5 110.1  0.08 20 13.8 0.08 20 6.240.11 12  CONT. — 91.9 — — 11.5 — — 5.59 — — LYD845 83399.3 — — — — — —6.06 0.36 5 CONT. — — — — — — — 5.79 — — LYD851 85197.1 60.4 0.41  4 7.55 0.41  4 — — — CONT. — 57.9 — —  7.23 — — — — — LYD803 85074.1 — —— — — — 5.18 0.39 9 LYD803 87327.1 — — — — — — 5.10 0.45 7 LYD80387331.3 59.6 0.10 13  7.45 0.10 13 5.04 0.23 6 CONT. — 52.6 — —  6.57 —— 4.76 — — Table 179. “CONT.”—Control; “Ave.”—Average; “% Incr.” = %increment; “p-val.”—p-value, L- p < 0.01.

TABLE 180 Genes showing improved plant performance at Normal growthconditions under regulation of At6669 promoter RGR Of Leaf RGR Of PlotRGR Of Rosette Number Coverage Diameter P- % P- % P- % Gene Name Event #Ave. Val. Incr. Ave. Val. Incr. Ave. Val. Incr. LYD869_H1 85983.1 — — —9.38 0.03 32 0.438 0.06 17 LYD859 83953.3 — — — — — — 0.416 0.20 11LYD859 83957.5 0.686 0.26 21 8.67 0.14 22 — — — LYD853 86496.1 — — —8.33 0.23 17 — — — LYD853 86497.7 — — — 8.68 0.13 22 — — — LYD82685587.2 0.685 0.27 21 8.56 0.16 20 0.411 0.27 10 LYD750 84966.3 — — —8.69 0.14 22 0.426 0.15 14 LYD744 86509.4 — — — — — — 0.411 0.27 10LYD699 85972.6 — — — 8.22 0.27 16 — — — CONT. — 0.566 — — 7.12 — — 0.374— — LYD908 84445.1 — — — 10.5 0.08 32 0.522 0.18 14 LYD908 84446.1 — — —9.62 0.23 21 — — — LYD908 84447.1 0.822 0.16 28 11.9 0.01 50 0.531 0.1216 LYD908 84447.4 — — — 11.7 0.01 48 0.550 0.06 20 LYD876 83416.3 0.7860.27 23 10.9 0.05 37 — — — LYD876 83417.3 — — — 10.0 0.15 27 — — —LYD876 83417.6 0.798 0.24 25 — — — — — — LYD876 83418.2 — — — 9.49 0.2820 — — — LYD865 83730.1 0.800 0.22 25 10.5 0.09 32 — — — LYD865 83733.5— — — 10.9 0.06 37 — — — LYD864 83406.2 — — — 9.78 0.23 23 — — — LYD86483406.4 — — — 9.54 0.26 20 — — — LYD864 83409.2 0.797 0.23 24 10.1 0.1627 — — — LYD864 83409.3 — — — 11.9 0.01 51 0.537 0.10 17 LYD843 83772.1— — — 10.6 0.08 33 0.530 0.13 16 LYD843 83774.1 — — — 9.79 0.21 23 — — —LYD843 83775.2 0.810 0.20 27 11.8 0.02 48 0.528 0.16 15 LYD843 83775.4 —— — 10.3 0.11 29 — — — LYD842 83528.2 0.813 0.20 27 9.85 0.19 24 — — —LYD835 84139.1 0.796 0.24 24 9.93 0.17 25 — — — LYD835 84141.3 — — —9.75 0.20 23 — — — LYD835 84143.1 0.790 0.26 23 — — — — — — LYD83584143.2 — — — 10.6 0.07 34 0.516 0.22 13 LYD821 84053.3 0.932 0.02 4612.3 L 55 0.542 0.08 18 LYD821 84054.1 0.800 0.20 25 11.1 0.04 39 — — —LYD821 84054.4 0.787 0.27 23 9.48 0.28 19 — — — LYD793 83499.7 0.8130.19 27 10.7 0.08 35 — — — LYD793 83500.4 0.801 0.20 25 10.5 0.08 33 — —— LYD777 83489.3 — — — 9.86 0.18 24 — — — LYD777 83492.3 — — — 9.75 0.2123 — — — LYD777 83492.4 — — — 9.44 0.29 19 — — — LYD777 83493.3 — — —10.8 0.06 36 — — — LYD767 83485.1 — — — 11.3 0.03 43 0.520 0.20 13LYD767 83486.2 0.775 0.28 21 10.5 0.08 32 0.509 0.28 11 LYD767 83488.1 —— — 9.70 0.22 22 — — — LYD767 83488.5 0.780 0.27 22 9.76 0.20 23 — — —LYD753 83916.1 — — — 10.2 0.12 29 0.509 0.28 11 LYD753 83917.6 0.8850.06 38 12.3 L 54 0.531 0.12 16 LYD735 84168.2 — — — 10.4 0.09 31 0.5100.26 11 LYD730 84258.1 0.895 0.05 40 10.7 0.06 35 0.529 0.14 15 LYD72984159.1 — — — 10.6 0.09 34 0.513 0.27 12 LYD729 84159.4 — — — 10.1 0.1427 — — — LYD729 84159.6 — — — 10.3 0.10 30 — — — LYD729 84160.3 — — —10.7 0.07 34 — — — LYD726 84591.1 0.776 0.28 21 12.3 L 55 0.532 0.12 16LYD726 84593.1 0.815 0.17 27 12.1 L 52 0.549 0.05 20 LYD726 84595.1 — —— 10.6 0.07 34 0.520 0.20 14 LYD726 84595.2 0.801 0.25 25 — — — — — —LYD726 84595.3 — — — 9.52 0.29 20 — — — LYD720 83763.1 0.770 0.30 2011.7 0.01 48 0.525 0.16 15 LYD720 83764.2 — — — 10.7 0.06 35 — — —LYD720 83764.3 0.814 0.18 27 10.5 0.08 32 0.518 0.21 13 LYD705 83384.4 —— — 9.45 0.28 19 — — — CONT. — 0.640 — — 7.94 — — 0.458 — — LGP4376951.2 0.758 0.17 10 — — — — — — LGP43 76953.5 0.735 0.08 7 — — — — — —LGP43 76955.1 0.733 0.20 7 — — — — — — LGP43 76955.2 0.756 0.28 10 8.690.17 8 0.375 0.14 5 CONT. — 0.687 — — 8.07 — — 0.357 — — LYD914 84179.2— — — 14.8 0.05 29 0.578 0.15 15 LYD914 84183.6 — — — 14.9 0.05 30 0.6110.04 21 LYD901 83883.3 — — — 13.5 0.26 17 0.568 0.24 13 LYD892 84250.7 —— — 16.2 0.01 41 0.583 0.13 16 LYD876 83418.3 — — — 14.0 0.14 21 0.5880.11 17 LYD864 83409.4 — — — 14.9 0.05 30 0.583 0.13 16 LYD843 83772.1 —— — 13.5 0.26 17 — — — LYD843 83775.2 — — — 14.6 0.12 27 0.567 0.30 12LYD842 83526.5 — — — 14.0 0.13 22 0.566 0.23 12 LYD755 84033.1 — — —13.9 0.18 21 — — — LYD753 83917.2 — — — 14.9 0.05 30 0.590 0.12 17LYD739 83386.2 — — — — — — 0.569 0.26 13 LYD735 84165.1 — — — 13.9 0.1621 0.563 0.25 12 LYD727 83791.1 — — — 13.6 0.21 18 — — — LYD727 83793.20.787 0.25 15 — — — — — — LYD727 83795.2 — — — 14.7 0.06 28 0.568 0.2213 LYD722 84944.3 — — — 14.6 0.08 27 0.574 0.22 14 LYD722 84944.4 — — —15.4 0.02 34 0.574 0.17 14 LYD720 83761.3 — — — 13.8 0.19 20 0.563 0.2812 LYD720 83763.1 — — — 13.5 0.25 17 0.561 0.27 11 CONT. — 0.682 — —11.5 — — 0.504 — — LGP25 75388.1 0.755 0.23 7 — — — — — — LGP1 76249.30.758 0.18 7 — — — — — — CONT. — 0.707 — — — — — — — — LYD922 83821.3 —— — 12.9 0.19 24 0.573 0.18 14 LYD922 83823.6 — — — 12.5 0.26 20 — — —LYD905 84145.3 — — — 12.9 0.20 23 — — — LYD905 84147.2 0.884 0.27 19 — —— — — — LYD901 83886.6 — — — 12.4 0.28 19 — — — LYD883 83912.2 0.8800.29 18 — — — — — — LYD883 83912.3 — — — 13.7 0.09 31 0.558 0.29 11LYD860 83625.4 0.950 0.10 28 12.4 0.28 19 — — — LYD836 83514.4 0.8850.25 19 13.2 0.15 26 0.567 0.23 13 LYD833 83513.5 0.876 0.28 18 12.50.26 20 — — — LYD811 83711.2 0.897 0.24 20 — — — — — — LYD755 84035.1 —— — 12.8 0.20 23 — — — LYD755 84035.2 0.969 0.06 30 12.4 0.28 19 — — —LYD739 83386.2 0.933 0.13 25 — — — — — — LYD725 84190.3 — — — 12.7 0.2222 0.563 0.23 12 LYD725 84191.1 — — — 12.5 0.27 19 — — — LYD704 83785.70.877 0.29 18 — — — — — — CONT. — 0.745 — — 10.4 — — 0.502 — — LYD92585844.1 — — — 13.9 0.09 30 0.607 0.17 16 LYD897 84444.13 — — — 12.8 0.2620 0.592 0.28 13 LYD897 84444.4 0.817 0.23 16 — — — — — — LYD897 84444.60.853 0.14 21 13.2 0.20 23 0.610 0.18 17 LYD869_H1 85983.1 — — — 13.60.13 27 0.623 0.10 19 LYD854 84992.3 0.841 0.16 20 — — — — — — LYD82685587.1 0.881 0.07 25 13.3 0.15 25 0.606 0.16 16 LYD824 83903.3 — — —14.3 0.06 34 0.659 0.03 26 LYD824 83905.3 — — — 14.2 0.06 33 0.611 0.1417 LYD824 83907.6 0.849 0.14 21 — — — — — — LYD816 85591.1 — — — 15.8 L48 0.695 L 33 LYD816 85594.2 0.897 0.06 28 — — — — — — LYD814 84971.20.802 0.29 14 — — — — — — LYD814 84973.6 0.852 0.12 21 — — — — — —LYD791 85129.4 0.874 0.09 24 13.8 0.10 29 0.608 0.16 16 LYD791 85129.5 —— — 13.3 0.15 25 0.637 0.06 22 LYD790 84574.2 0.839 0.15 19 16.6 L 550.675 0.01 29 LYD774 83938.4 — — — 12.9 0.22 21 — — — LYD774 83940.2 — —— 13.6 0.11 27 — — — LYD769 84121.5 — — — 13.7 0.11 28 0.606 0.18 16LYD769 84123.1 — — — 14.2 0.06 33 0.598 0.21 14 LYD769 84123.3 — — —14.2 0.07 33 0.618 0.12 18 LYD756 85067.2 — — — 12.7 0.27 19 — — —LYD756 85069.8 — — — 12.6 0.29 18 — — — LYD752 85049.1 — — — 13.7 0.1028 0.610 0.15 17 LYD741 84429.4 0.804 0.30 14 — — — — — — LYD702 84412.3— — — 12.9 0.25 21 0.593 0.30 13 CONT. — 0.703 — — 10.7 — — 0.523 — —LYD809 83507.2 0.735 0.18 22 — — — — — — LYD726 84595.3 0.730 0.19 21 —— — — — — LYD701 84068.1 0.713 0.27 19 — — — — — — CONT. — 0.602 — — — —— — — — LYD874 85656.1 0.786 0.28 18 — — — — — — LYD834 84452.1 — — —12.1 0.30 18 — — — LYD829 85058.4 0.789 0.28 19 — — — — — — LYD82985058.8 0.797 0.27 20 — — — — — — LYD806 85557.1 — — — 14.8 0.01 450.617 0.06 22 LYD798 84533.4 — — — 13.1 0.10 29 0.604 0.09 19 LYD76585811.2 0.825 0.17 24 — — — — — — LYD762 85112.5 0.865 0.08 30 12.8 0.1326 0.585 0.16 16 LYD762 85114.3 — — — 13.7 0.05 34 0.605 0.08 19 LYD76285114.4 0.812 0.24 22 12.6 0.20 24 0.575 0.29 13 LYD754 85597.2 — — —13.0 0.11 27 0.570 0.26 12 LYD751 85720.3 0.813 0.19 23 — — — — — —LYD749 84423.6 — — — — — — 0.609 0.09 20 LYD711 85315.1 0.824 0.17 24 —— — — — — LYD711 85316.5 0.790 0.28 19 14.1 0.04 38 0.617 0.06 22 CONT.— 0.664 — — 10.2 — — 0.507 — — LYD925 85840.1 0.659 0.27 23 6.98 0.30 150.401 0.10 17 LYD925 85844.1 — — — 7.38 0.14 21 0.414 0.06 21 LYD92486507.1 — — — 7.60 0.09 25 0.407 0.09 18 LYD884 84579.2 — — — — — —0.383 0.27 11 LYD879 85963.1 — — — 7.95 0.05 31 0.383 0.28 11 LYD87884488.5 — — — 7.28 0.17 20 0.389 0.21 13 LYD878 84488.8 — — — 7.23 0.2019 — — — LYD834 84452.3 — — — 7.62 0.09 25 0.401 0.11 17 LYD834 84452.4— — — 7.32 0.16 20 0.394 0.17 15 LYD829 85058.3 — — — 7.82 0.06 29 0.3980.16 16 LYD829 85059.2 — — — 8.02 0.03 32 0.401 0.11 17 LYD829 85059.3 —— — 6.99 0.29 15 — — — LYD813 83725.1 — — — 7.25 0.18 19 — — — LYD81383725.2 — — — 7.16 0.22 18 — — — LYD804 84134.1 — — — 7.84 0.05 29 0.3810.29 11 LYD804 84138.5 — — — 7.32 0.18 20 0.386 0.25 12 LYD798 84533.3 —— — 7.26 0.18 19 — — — LYD798 84533.5 — — — — — — 0.393 0.17 14 LYD79884533.6 — — — 7.42 0.13 22 — — — LYD784 86519.3 — — — 8.08 0.05 33 0.3940.27 15 LYD780 86514.2 — — — 7.61 0.09 25 — — — LYD757 83470.5 — — —7.59 0.10 25 0.399 0.13 16 LYD757 83473.4 — — — 7.59 0.09 25 — — —LYD754 85597.1 — — — 8.60 0.01 41 0.409 0.09 19 LYD754 85597.2 — — —7.59 0.09 25 — — — LYD754 85598.1 — — — — — — 0.380 0.30 11 LYD75185720.2 — — — — — — 0.388 0.23 13 LYD751 85720.3 — — — 8.07 0.03 330.397 0.13 16 LYD751 85722.1 — — — 7.30 0.16 20 — — — LYD751 85722.2 — —— 7.15 0.22 17 — — — LYD751 85724.1 0.676 0.21 26 — — — — — — LYD72284941.2 — — — 7.25 0.18 19 — — — LYD722 84945.1 0.655 0.25 22 — — — — —— LYD702 84412.3 — — — 7.61 0.08 25 — — — CONT. — 0.536 — — 6.09 — —0.344 — — LGP49 77651.3 0.746 0.20 16 — — — — — — LGP49 77651.4 0.7270.22 13 — — — — — — LGP49 77651.8 0.795 0.02 24 — — — — — — LGP4977652.6 — — — 9.15 0.07 19 — — — LGP49 77652.8 0.755 0.11 18 — — — — — —CONT. — 0.642 — — 7.71 — — — — — LGP25 75389.4 — — — — — — 0.449 0.13 10LGP25 75390.4 — — — — — — 0.444 0.12 8 LGP25 75391.4 0.766 0.15 5 — — —0.430 0.16 5 LGP1 76250.4 — — — — — — 0.425 0.06 4 CONT. — 0.732 — — — —— 0.409 — — LGP44 75764.8 0.746 0.24 10 7.74 0.04 11 0.329 0.02 7 LGP1075385.3 0.730 0.29 8 7.69 0.25 11 0.334 0.09 9 CONT. — 0.678 — — 6.95 —— 0.307 — — LGP8 75409.5 0.840 0.02 19 — — — — — — LGP20 76941.5 0.7700.28 9 13.2 0.10 20 0.493 0.29 10 LGP20 76945.4 0.745 0.30 6 — — — — — —CONT. — 0.705 — — 11.0 — — 0.446 — — LYD841 85885.2 — — — — — — 0.4020.43 7 CONT. — — — — — — — 0.374 — — LYD926 83826.2 0.765 0.41 15 — — —— — — LYD926 83830.2 0.756 0.42 14 — — — — — — CONT. — 0.664 — — — — — —— — LYD845 83397.6 — — — 13.2 0.36 15 — — — CONT. — — — — 11.5 — — — — —LYD850 86628.1 0.789 0.37 17 — — — — — — CONT. — 0.673 — — — — — — — —LYD803 85074.1 — — — — — — 0.582 0.26 15 LYD803 87331.3 — — — 9.47 0.3117 0.563 0.36 12 CONT. — — — — 8.11 — — 0.505 — — Table 180.“CONT.”—Control; “Ave.”—Average; “% Incr.” = % increment;“p-val.”—p-value, L- p < 0.01.

Example 28 Evaluating Transgenic Arabidopsis Under Normal ConditionsUsing Seedling Analyses of T2 and T1 Plants

Surface sterilized seeds were sown in basal media [50% Murashige-Skoogmedium (MS) supplemented with 0.8% plant agar as solidifying agent] inthe presence of Kanamycin (used as a selecting agent). After sowing,plates were transferred for 2-3 days for stratification at 4° C. andthen grown at 25° C. under 12-hour light 12-hour dark daily cycles for 7to 10 days. At this time point, seedlings randomly chosen were carefullytransferred to plates containing ½ MS media (15 mM N, normalconditions). For experiments performed in T₂ lines, each plate contained5 seedlings of the same transgenic event, and 3-4 different plates(replicates) for each event. For each polynucleotide of the invention atleast four-five independent transformation events were analyzed fromeach construct. For experiments performed in T₁ lines, each platecontained 5 seedlings of 5 independent transgenic events and 3-4different plates (replicates) were planted. In total, for T₁ lines, 20independent events were evaluated. Plants expressing the polynucleotidesof the invention were compared to the average measurement of the controlplants (empty vector or GUS reporter gene under the same promoter) usedin the same experiment.

Digital Imaging—

A laboratory image acquisition system, which consists of a digitalreflex camera (Canon EOS 300D) attached with a 55 mm focal length lens(Canon EF-S series), mounted on a reproduction device (Kaiser RS), whichincludes 4 light units (4×150 Watts light bulb) and located in adarkroom, was used for capturing images of plantlets sawn in agarplates.

The image capturing process was repeated every 3-4 days starting at day1 till day 10 (see for example the images in FIGS. 3A-F). An imageanalysis system was used, which consists of a personal desktop computer(Intel P4 3.0 GHz processor) and a public domain program—ImageJ 1.39[Java based image processing program which was developed at the U.S.National Institutes of Health and freely available on the internet atrsbweb (dot) nih (dot) gov/]. Images were captured in resolution of 10Mega Pixels (3888×2592 pixels) and stored in a low compression JPEG(Joint Photographic Experts Group standard) format. Next, analyzed datawas saved to text files and processed using the JMP statistical analysissoftware (SAS institute).

Seedling Analysis—

Using the digital analysis seedling data was calculated, including leafarea, root coverage and root length.

The relative growth rate for the various seedling parameters wascalculated according to the following Formulas XIII (RGR leaf area,above), XXVIII (RGR root coverage, described above) and VI (RGR rootlength, below).

At the end of the experiment, plantlets were removed from the media andweighed for the determination of plant fresh weight. Plantlets were thendried for 24 hours at 60° C., and weighed again to measure plant dryweight for later statistical analysis. The fresh and dry weights wereprovided for each Arabidopsis plant. Growth rate was determined bycomparing the leaf area coverage, root coverage and root length, betweeneach couple of sequential photographs, and results were used to resolvethe effect of the gene introduced on plant vigor under optimalconditions. Similarly, the effect of the gene introduced on biomassaccumulation, under optimal conditions, was determined by comparing theplants' fresh and dry weight to that of control plants (containing anempty vector or the GUS reporter gene under the same promoter). Fromevery construct created, 3-5 independent transformation events wereexamined in replicates.

Statistical Analyses—

To identify genes conferring significantly improved plant vigor orenlarged root architecture, the results obtained from the transgenicplants were compared to those obtained from control plants. To identifyoutperforming genes and constructs, results from the independenttransformation events tested were analyzed separately. To evaluate theeffect of a gene event over a control the data was analyzed by Student'st-test and the p value was calculated. Results were consideredsignificant if p≦0.1. The JMP statistics software package was used(Version 5.2.1, SAS Institute Inc., Cary, N.C., USA).

Experimental Results:

Tables 181-183 summarize the observed phenotypes of transgenic plantsexpressing the gene constructs using the TC-T2 assays [tissue culture(TC), T2 plants, seedling (plantlets) analyses].

The genes presented in Table 181 showed a significant improvement asthey produced larger plant biomass (plant fresh and dry weight) in T2generation when grown under normal growth conditions, compared tocontrol plants. The genes were cloned under the regulation of aconstitutive promoter (At6669, SEQ ID NO: 15751). The evaluation of eachgene was carried out by testing the performance of different number ofevents. Some of the genes were evaluated in more than one tissue cultureassay. The results obtained in these second experiments weresignificantly positive as well.

TABLE 181 Genes showing improved plant performance at Normal growthconditions under regulation of At6669 promoter Dry Weight [mg] FreshWeight [mg] Gene P- P- Name Event # Ave. Val. % Incr. Ave. Val. % Incr.LYD921 87628.1 6.68 0.06 58 124.9 0.15 50 LYD918 85320.1 4.95 0.10 1794.2 0.11 13 LYD918 85321.2 7.52 0.02 78 133.2 0.03 60 LYD890 87185.14.65 0.20 10 — — — LYD890 87189.1 — — — 97.6 0.10 17 LYD890 87190.2 4.830.09 14 101.7 L 22 LYD880 85204.3 4.70 0.28 11 — — — LYD873 83410.3 5.150.23 22 — — — LYD873 83410.6 5.12 0.25 21 — — — LYD873 83414.1 5.88 0.0439 100.0 0.11 20 LYD855 84609.3 10.4 0.02 147 185.8 0.02 123 LYD85584609.4 8.97 0.15 112 148.3 0.15 78 LYD855 84610.2 8.65 L 104 125.5 L 51LYD855 86525.2 4.80 0.28 13 — — — LYD837 83392.1 4.95 0.07 17 98.2 0.1718 LYD815 84416.1 5.50 0.08 30 100.0 0.08 20 LYD815 84416.3 6.83 0.03 61124.9 0.04 50 LYD815 84417.1 5.03 0.15 19 96.4 0.25 16 LYD796 87620.65.38 0.04 27 100.8 0.02 21 LYD796 87623.3 5.28 0.14 24 97.9 0.03 18LYD771 85463.1 5.65 0.03 33 108.6 0.06 30 LYD771 85463.2 — — — 99.4 0.1619 LYD771 85463.3 8.50 L 101 155.5 0.01 87 LYD771 85463.4 5.70 0.13 35102.2 0.29 23 CONT. — 4.24 — — 83.3 — — MGP5 84025.4 5.60 0.18 19 — — —MGP4 84018.3 6.10 L 30 106.0 0.11 23 MGP14 85217.2 6.00 0.11 28 105.80.09 23 MGP13 84007.2 5.77 0.11 23 95.1 0.12 11 MGP13 84007.5 7.07 L 51113.2 0.01 32 MGP13 84010.3 5.88 0.06 25 104.0 L 21 MGP12 84001.1 — — —96.8 0.08 13 MGP12 84005.1 5.33 0.22 14 95.3 0.21 11 MGP1 84554.2 6.10 L30 111.8 0.16 30 CONT. — 4.69 — — 85.9 — — LYD887 84746.1 7.35 0.01 74131.7 0.02 59 LYD868 86633.2 6.42 0.05 53 131.2 0.07 58 LYD868 86673.24.53 0.28 7 86.8 0.29 5 LYD861 85566.3 5.10 0.05 21 94.5 0.10 14 LYD86185568.1 5.00 0.07 19 97.8 0.13 18 LYD861 85568.6 4.72 0.15 12 93.1 0.0312 LYD818 87321.4 5.38 0.30 28 107.7 0.30 30 LYD818 87323.2 5.15 0.18 22101.7 0.14 23 LYD817 86926.3 9.48 L 125 157.5 L 90 LYD817 86927.1 5.150.07 22 — — — LYD773 87162.2 5.77 0.05 37 102.5 0.14 24 LYD773 87165.46.90 L 64 136.6 L 65 LYD768 87156.1 5.20 0.06 23 105.8 0.02 27 LYD76887160.4 4.68 0.29 11 95.7 0.04 15 LYD721 87318.4 5.58 0.16 32 101.0 0.2222 CONT. — 4.21 — — 83.0 — — MGP9 87204.2 7.28 L 74 131.4 L 54 MGP987205.3 5.45 0.15 31 — — — MGP9 87206.1 5.12 0.23 23 101.3 0.25 19 MGP987208.1 5.20 0.18 25 100.7 0.25 18 CONT. — 4.17 — — 85.4 — — LGP8585845.1 4.42 0.04 46 83.5 0.01 76 LGP85 85846.1 4.38 0.06 45 — — — LGP8585846.3 4.95 0.05 64 100.3 L 112 LGP85 85846.5 5.38 L 78 120.1 L 154LGP85 85849.1 4.45 L 47 — — — LGP105 85298.2 6.12 L 102 — — — LGP10585298.3 4.38 L 45 95.3 L 101 LGP105 85298.4 5.42 L 79 98.7 L 108 LGP10585298.5 5.17 L 71 105.3 L 122 LGP105 85298.7 5.28 0.07 74 116.2 0.02 145LGP102 85929.1 — — — 66.7 0.19 41 LGP102 85930.3 3.58 0.08 18 73.0 0.0754 LGP102 85931.2 3.90 0.10 29 — — — LGP102 85933.2 5.15 0.07 70 — — —CONT. — 3.02 — — 47.3 — — LGP99 85617.3 8.18 0.13 23 162.2 0.17 27 LGP9883620.5 — — — 146.9 0.20 15 LGP98 83620.7 8.18 0.06 23 149.7 0.14 17LGP87 85864.1 10.0 0.01 51 195.2 0.02 53 LGP86 84346.3 9.50 L 43 175.3 L38 LGP83 85755.1 8.30 0.26 25 — — — LGP83 85759.2 — — — 142.8 0.14 12LGP83 85759.4 7.65 0.16 15 145.4 0.17 14 LGP110 85612.1 8.27 0.24 25184.3 0.25 45 LGP107 84338.1 8.15 0.03 23 164.1 0.20 29 LGP106 85865.2 —— — 149.2 0.28 17 LGP106 85869.2 8.00 0.04 21 155.8 0.05 22 LGP10185292.1 7.35 0.20 11 138.6 0.27 9 CONT. — 6.62 — — 127.4 — — MGP985224.1 5.88 0.08 31 113.5 0.12 40 MGP7 86141.3 5.05 0.24 13 — — — MGP786141.4 — — — 98.4 0.13 21 CONT. — 4.47 — — 81.1 — — LYD857 86674.1 — —— 115.3 0.17 16 LYD856 85693.2 12.5 L 118 200.1 L 101 LYD855 84609.312.0 0.01 108 187.0 L 88 LYD852 85819.3 — — — 118.8 0.04 19 LYD81084436.2 9.07 0.08 58 158.7 0.06 59 LYD807 84080.1 — — — 116.3 0.20 17LYD802 85132.1 7.70 0.05 34 133.1 0.03 34 LYD792 85553.1 7.30 0.12 27129.4 0.04 30 LYD694 84125.1 9.20 0.04 60 157.3 0.02 58 CONT. — 5.74 — —99.5 — — LYD907 84978.1 6.65 0.02 74 108.5 L 46 LYD906 84750.1 5.45 0.0343 100.0 0.12 35 LYD906 84754.1 4.62 0.19 21 — — — LYD904 84498.4 5.33 L40 103.0 L 39 LYD904 84499.2 4.90 0.06 29 88.9 0.18 20 LYD903 85544.34.92 0.02 29 94.1 L 27 LYD903 85544.5 4.45 0.14 17 — — — LYD902 84948.54.85 0.24 27 — — — LYD890 87189.1 4.25 0.25 11 80.9 0.21 9 LYD87884487.3 5.07 L 33 97.8 L 32 LYD878 84488.8 5.17 0.14 36 95.8 0.13 29LYD867 85535.1 5.40 L 42 106.4 0.09 43 LYD858 85796.1 4.38 0.21 15 84.40.09 14 LYD858 85797.1 6.22 L 63 132.1 0.02 78 LYD856 85693.2 4.60 0.0321 90.2 0.07 21 LYD844 85192.7 4.45 0.07 17 — — — LYD825 85883.3 4.830.04 27 87.3 0.25 17 LYD812 85563.4 4.83 L 27 102.1 0.09 37 LYD81285564.1 4.28 0.29 12 — — — LYD802 85132.1 5.65 L 48 — — — LYD719 85261.24.17 0.16 10 80.9 0.29 9 LYD718 85458.3 5.07 0.17 33 91.3 0.16 23 LYD69985973.1 5.30 0.03 39 94.5 L 27 CONT. — 3.81 — — 74.3 — — LGP82 83662.24.75 0.20 18 — — — LGP81 84957.3 4.90 0.12 22 — — — LGP77 81453.2 5.70 L42 — — — LGP75 85309.4 6.47 L 61 190.4 0.10 50 LGP74 81325.1 5.17 0.0329 — — — LGP73 81449.1 5.38 0.01 34 — — — LGP73 81449.3 4.83 0.03 20 — —— LGP72 85854.4 5.00 0.24 24 — — — LGP71 82502.3 4.75 0.27 18 — — —CONT. — 4.03 — — 127.2 — — LGP90 85764.5 7.62 0.32 15 146.7 0.39 15CONT. — 6.62 — — 127.4 — — Table 181. “CONT.”—Control; “Ave.”—Average;“% Incr.” = % increment; “p-val.”—p-value, L- p < 0.01.

The genes presented in Tables 182 and 183 below show a significantimprovement in plant performance since they produced a larger leafbiomass (leaf area) and root biomass (root length and root coverage)(Table 182) and a higher relative growth rate of leaf area, rootcoverage and root length (Table 183) when grown under normal growthconditions, compared to control plants. Plants producing larger rootbiomass have better possibilities to absorb larger amount of nitrogenfrom soil. Plants producing larger leaf biomass have better ability toproduce assimilates. The genes were cloned under the regulation of aconstitutive promoter (At6669). The evaluation of each gene wasperformed by testing the performance of different number of events. Someof the genes were evaluated in more than one seedling analysis. Thissecond experiment confirmed the significant increment in leaf and rootperformance. Event with p-value<0.1 was considered statisticallysignificant.

TABLE 182 Genes showing improved plant performance at Normal growthconditions under regulation of At6669 promoter Roots Coverage Leaf Area[cm²] [cm²] Roots Length [cm] Gene P- % P- % P- % Name Event # Ave. Val.Incr. Ave. Val. Incr. Ave. Val. Incr. LYD921 87628.1 0.518 0.27 20 — — —— — — LYD918 85321.2 0.587 0.02 36 6.29 0.12 31 — — — LYD890 87185.1 — —— 6.32 0.05 32 6.62 0.30 11 LYD873 83410.3 — — — 5.88 0.20 23 — — —LYD873 83410.6 — — — 6.34 0.20 32 — — — LYD855 84609.3 0.598 0.03 38 — —— — — — LYD837 83390.5 — — — 6.03 0.18 26 — — — LYD837 83390.8 — — —7.13 0.04 49 — — — LYD815 84416.3 0.561 0.06 30 6.93 0.12 45 6.75 0.2013 LYD796 87620.6 — — — 6.14 0.05 28 — — — LYD796 87623.3 — — — 5.490.29 15 — — — LYD771 85463.1 0.477 0.18 10 6.10 0.07 27 — — — LYD77185463.3 0.692 L 60 8.41 0.04 76 6.75 0.26 13 LYD771 85463.4 0.530 0.2822 6.56 0.20 37 6.66 0.29 12 CONT. — 0.432 — — 4.79 — — 5.96 — — MGP584022.3 — — — 6.33 0.19 16 6.36 0.03 12 MGP5 84025.7 — — — 6.76 0.12 246.51 0.17 15 MGP4 84018.3 0.556 0.03 21 7.36 0.01 35 6.99 L 24 MGP484019.5 — — — — — — 6.29 0.18 11 MGP4 84020.2 — — — 6.23 0.24 14 6.320.15 12 MGP2 84014.5 — — — — — — 6.09 0.29 8 MGP14 85217.2 0.590 0.04 28— — — — — — MGP13 84007.2 0.560 0.06 22 — — — — — — MGP13 84007.5 0.642L 39 6.91 0.04 27 6.41 0.09 13 MGP13 84010.3 0.570 0.04 24 6.36 0.21 17— — — MGP13 84010.4 — — — 6.18 0.20 13 6.36 0.06 12 MGP12 84001.1 — — —6.39 0.14 17 6.81 0.04 20 MGP12 84004.4 0.551 0.15 20 7.68 0.19 41 6.830.01 21 MGP1 84554.2 0.544 0.04 18 6.48 0.17 19 6.32 0.06 12 CONT. —0.461 — — 5.45 — — 5.66 — — LYD887 84745.1 0.502 0.17 12 6.53 0.19 11 —— — LYD887 84746.1 0.633 0.02 41 9.26 0.02 57 6.93 0.08 15 LYD86886633.2 0.575 0.05 28 8.37 0.14 42 — — — LYD868 86673.1 — — — 7.24 0.2923 — — — LYD861 85566.3 0.492 0.08 10 — — — — — — LYD861 85568.1 0.5330.09 19 — — — — — — LYD818 87321.2 — — — 6.95 0.22 18 6.89 0.10 15LYD818 87321.4 0.532 0.25 19 — — — — — — LYD818 87323.2 — — — 9.34 0.1059 6.77 0.16 13 LYD817 86926.3 0.711 L 59 9.30 L 58 6.63 0.15 10 LYD81786927.1 0.571 L 27 7.67 0.10 30 6.62 0.16 10 LYD773 87162.2 0.533 0.0719 7.15 0.12 21 — — — LYD773 87165.4 0.673 L 50 9.77 L 66 7.30 L 21LYD768 87156.1 0.512 0.03 14 7.12 0.14 21 — — — LYD768 87157.2 0.4850.08 8 — — — — — — LYD768 87160.4 0.496 0.29 11 — — — — — — LYD72187318.2 — — — 7.50 0.07 27 6.92 0.06 15 LYD721 87318.3 — — — 6.76 0.1715 6.61 0.16 10 LYD721 87318.4 0.530 0.12 18 8.38 0.09 42 6.73 0.07 12LYD721 87320.1 — — — — — — 6.46 0.26 7 CONT. — 0.448 — — 5.89 — — 6.01 —— MGP9 87204.2 0.596 L 38 — — — — — — CONT. — 0.433 — — — — — — — —LGP85 85845.1 0.402 0.03 35 6.85 0.02 45 — — — LGP85 85846.1 0.414 0.0339 5.65 0.14 19 — — — LGP85 85846.3 0.418 0.04 40 7.11 0.09 50 6.94 0.2911 LGP85 85846.5 0.425 L 42 7.70 0.06 63 — — — LGP85 85849.1 0.378 L 277.39 0.02 56 6.77 0.30 9 LGP105 85298.2 0.466 L 56 7.64 L 61 6.74 0.24 8LGP105 85298.3 0.384 L 28 7.66 L 62 — — — LGP105 85298.4 0.462 L 55 8.46L 79 7.61 L 22 LGP105 85298.5 0.421 L 41 7.40 0.01 56 — — — LGP10585298.7 0.420 0.03 41 5.69 0.15 20 — — — LGP102 85930.3 0.353 L 18 — — —— — — LGP102 85931.2 0.368 0.08 23 — — — — — — LGP102 85933.2 0.433 0.0845 6.22 0.04 31 — — — LGP102 85933.3 0.343 0.04 15 — — — — — — CONT. —0.299 — — 4.73 — — 6.23 — — LGP99 85617.3 0.679 0.04 32 — — — — — —LGP98 83620.7 0.623 0.04 21 — — — — — — LGP97 83609.1 0.581 0.12 13 — —— — — — LGP97 83611.2 — — — — — — 6.27 0.29 5 LGP95 83695.2 — — — — — —6.68 0.26 12 LGP87 85864.1 0.692 0.01 35 — — — — — — LGP86 84346.3 0.6520.03 27 — — — — — — LGP83 85755.1 0.687 0.13 34 — — — — — — LGP8385759.2 0.618 0.06 20 7.98 0.03 18 6.38 0.14 7 LGP83 85759.4 0.599 0.0817 — — — 6.85 0.01 15 LGP110 85611.1 — — — — — — 6.60 0.24 11 LGP11085612.1 0.651 0.11 27 — — — — — — LGP107 84338.1 0.628 L 22 8.09 0.10 196.75 0.16 13 LGP106 85865.2 0.589 0.28 15 — — — — — — LGP106 85869.20.594 0.10 16 8.46 0.05 25 — — — LGP100 83691.2 — — — — — — 6.64 0.22 11LGP100 83691.6 — — — — — — 6.43 0.16 8 LGP100 83691.8 — — — — — — 6.240.20 5 CONT. — 0.514 — — 6.78 — — 5.97 — — MGP9 85224.1 0.471 0.03 22 —— — — — — MGP7 86137.1 0.471 0.05 22 — — — — — — MGP7 86141.3 0.426 0.2810 — — — — — — CONT. — 0.386 — — — — — — — — LYD918 85320.2 — — — 7.830.11 33 6.78 0.02 19 LYD910 85212.1 — — — 6.98 0.21 19 6.44 0.19 13LYD880 85204.3 — — — — — — 6.10 0.14 7 LYD858 85796.1 0.561 0.21 10 7.45L 27 6.61 0.02 16 LYD857 86635.1 — — — 7.86 0.02 33 6.63 L 16 LYD85786674.1 — — — 8.97 L 52 7.20 L 26 LYD856 85693.2 0.976 L 91 11.3 L 917.23 0.01 27 LYD855 84609.3 0.784 0.01 53 9.01 0.02 53 — — — LYD85285816.1 — — — — — — 6.00 0.14 5 LYD852 85816.2 — — — 6.67 0.13 13 6.140.23 8 LYD852 85819.3 0.578 0.21 13 6.94 0.19 18 6.41 0.19 12 LYD81584416.1 — — — 6.75 0.23 15 6.89 0.02 21 LYD815 84416.2 0.643 0.14 26 — —— — — — LYD815 84416.3 — — — — — — 6.16 0.23 8 LYD810 84436.2 0.757 L 488.97 L 52 6.68 L 17 LYD810 84437.10 — — — — — — 5.95 0.26 4 LYD81084437.5 — — — 8.18 L 39 6.88 0.02 21 LYD807 84078.1 0.546 0.27 7 — — — —— — LYD807 84080.1 0.654 0.05 28 8.66 L 47 6.87 L 20 LYD802 85132.10.709 0.14 39 — — — 6.81 0.11 19 LYD801 84618.4 — — — 8.65 0.05 47 6.900.11 21 LYD792 85550.1 — — — — — — 6.30 0.22 10 LYD792 85553.1 0.679 L33 8.18 0.02 39 6.88 L 21 LYD785 84430.1 — — — 7.40 0.18 26 6.72 0.09 18LYD785 84430.5 — — — — — — 6.07 0.21 6 LYD785 84430.6 — — — — — — 6.120.19 7 LYD785 84430.7 — — — 7.47 0.04 27 6.90 0.03 21 LYD782 85902.1 — —— 7.18 0.24 22 — — — LYD782 85903.1 — — — 8.10 0.03 38 6.46 0.22 13LYD782 85904.3 — — — 6.66 0.23 13 — — — LYD771 85463.1 — — — — — — 6.560.10 15 LYD771 85463.3 — — — 7.53 0.06 28 6.51 0.03 14 LYD771 85463.40.605 0.28 18 7.50 0.19 27 6.49 0.19 14 LYD723 84940.4 — — — 8.28 0.0541 6.88 0.07 21 LYD719 85261.3 — — — — — — 5.96 0.26 4 LYD707 85707.10.561 0.16 10 7.81 0.01 33 6.85 L 20 LYD694 84125.1 0.707 0.02 38 9.03 L53 6.02 0.10 5 CONT. — 0.512 — — 5.89 — — 5.71 — — LYD921 87628.1 0.3810.23 15 — — — — — — LYD910 87192.4 0.375 0.21 13 — — — — — — LYD90784978.1 0.512 L 54 — — — — — — LYD906 84750.1 0.443 L 33 5.50 0.18 23 —— — LYD906 84752.3 0.418 0.22 26 — — — — — — LYD906 84754.1 0.439 0.1332 — — — — — — LYD904 84498.4 0.467 L 40 — — — — — — LYD904 84499.20.453 0.04 36 5.84 0.06 30 6.58 0.03 18 LYD903 85544.3 0.441 L 33 5.460.15 22 — — — LYD903 85544.5 — — — 5.04 0.21 12 — — — LYD902 84948.30.422 L 27 — — — 6.07 0.24 9 LYD902 84948.5 0.380 0.19 14 — — — — — —LYD890 87185.1 0.363 0.18 9 — — — — — — LYD890 87189.1 0.389 0.11 17 — —— — — — LYD878 84487.3 0.419 0.02 26 5.22 0.16 17 — — — LYD878 84488.80.485 0.10 46 5.71 0.15 28 — — — LYD867 85535.1 0.440 0.11 32 — — — — —— LYD858 85796.1 0.414 0.02 25 — — — — — — LYD858 85797.1 0.488 L 475.33 0.16 19 — — — LYD856 85693.2 0.434 L 30 — — — — — — LYD844 85192.70.369 0.24 11 — — — — — — LYD825 85883.1 0.365 0.22 10 — — — — — —LYD825 85883.3 0.389 0.15 17 — — — — — — LYD825 85884.2 0.381 0.05 15 —— — — — — LYD812 85560.2 0.464 0.07 40 5.24 0.19 17 6.54 0.09 17 LYD81285563.4 0.424 L 27 — — — — — — LYD812 85564.1 0.402 0.10 21 — — — — — —LYD802 85132.1 0.450 0.01 35 — — — — — — LYD792 85553.1 0.528 0.04 59 —— — — — — LYD719 87356.3 0.381 0.13 14 5.33 0.17 19 6.26 0.25 12 LYD71885458.3 0.442 0.11 33 — — — — — — LYD707 85707.1 0.384 0.10 16 — — — — —— LYD699 85973.1 0.395 0.02 19 — — — — — — CONT. — 0.333 — — 4.48 — —5.59 — — LGP82 83662.2 0.436 L 20 6.46 0.01 37 6.52 0.28 8 LGP82 83664.1— — — — — — 6.94 L 14 LGP82 83666.2 — — — 6.23 L 33 7.11 L 17 LGP8184957.3 0.446 L 23 7.46 L 59 7.44 L 23 LGP81 84957.8 0.382 0.25 5 5.410.11 15 6.55 0.26 8 LGP79 82510.1 — — — 5.90 L 26 — — — LGP79 82510.20.381 0.08 5 6.66 0.05 42 7.34 L 21 LGP79 82512.1 — — — 6.09 0.12 306.89 0.11 14 LGP79 82513.4 — — — 5.89 L 25 7.04 0.04 16 LGP78 82507.1 —— — 5.24 0.13 12 6.74 0.14 11 LGP78 82507.4 0.422 0.26 17 6.64 0.03 416.83 0.07 13 LGP78 82508.1 0.396 0.09 9 5.58 0.02 19 6.61 0.16 9 LGP7781452.2 — — — 5.47 0.08 16 6.73 0.19 11 LGP77 81453.2 0.449 L 24 6.130.08 31 — — — LGP77 81453.3 — — — 5.84 0.11 24 6.72 0.11 11 LGP7781454.1 0.435 0.11 20 6.36 0.05 35 7.01 0.05 16 LGP76 83653.1 — — — 5.350.18 14 — — — LGP76 83653.2 0.440 0.04 22 6.04 0.20 29 — — — LGP7683653.3 0.457 0.15 26 6.77 0.01 44 6.82 0.17 12 LGP76 83654.1 — — — 6.480.16 38 — — — LGP75 85309.1 — — — — — — 7.04 L 16 LGP75 85309.4 0.507 L40 8.43 0.01 80 7.24 L 19 LGP74 81324.2 — — — 5.59 0.23 19 — — — LGP7481325.1 0.453 0.03 25 7.87 L 68 7.03 0.05 16 LGP74 81326.4 — — — — — —6.43 0.19 6 LGP74 81328.1 — — — 5.43 0.09 16 6.87 L 13 LGP73 81449.10.495 L 37 8.11 L 73 7.78 L 28 LGP71 82500.4 0.402 0.24 11 6.89 L 477.38 L 22 LGP71 82502.2 — — — — — — 6.92 0.07 14 LGP71 82502.3 0.4670.04 29 6.20 L 32 6.92 L 14 LGP71 82502.4 — — — 5.37 0.12 14 — — — CONT.— 0.362 — — 4.70 — — 6.07 — — LGP94 84352.6 0.565 0.46 10 — — — — — —LGP111 83612.3 — — — — — — 6.64 0.45 11 LGP111 83616.5 — — — — — — 6.510.31 9 CONT. — 0.514 — — — — — 5.97 — — LGP96 88003 0.180 L 13 — — —0.871 0.04 15 LGP104 87557 0.159 0.07 11 — — — — — — CONT. — 0.138 — — —— — 0.593 — — Table 182. “CONT.”—Control; “Ave.”—Average; “% Incr.” = %increment; “p-val.”—p-value, L- p < 0.01.

TABLE 183 Genes showing improved plant performance at Normal growthconditions under regulation of At6669 promoter RGR Of Roots RGR Of RootRGR Of Leaf Area Coverage Length Gene P- % P- % P- % Name Event # Ave.Val. Incr. Ave. Val. Incr. Ave. Val. Incr. MGP5 84022.3 — — — 0.728 0.1217 0.546 0.06 20 MGP5 84025.6 — — — — — — 0.537 0.13 18 MGP5 84025.7 — —— 0.786 0.03 26 0.579 0.04 27 MGP4 84018.3 0.0509 0.13 20 0.836 L 340.585 L 28 MGP4 84020.2 — — — 0.716 0.19 15 — — — MGP2 84014.1 — — — — —— 0.517 0.23 13 MGP2 84014.5 — — — — — — 0.538 0.10 18 MGP14 85217.20.0514 0.17 21 — — — — — — MGP13 84007.2 0.0543 0.06 28 — — — — — —MGP13 84007.5 0.0619 L 46 0.797 0.01 28 0.575 0.02 26 MGP13 84010.30.0553 0.03 30 0.748 0.10 20 0.531 0.21 16 MGP13 84010.4 — — — 0.7200.14 15 0.541 0.08 19 MGP12 84001.1 — — — 0.744 0.08 19 0.577 0.03 26MGP12 84004.4 0.0520 0.17 22 0.893 L 43 0.564 0.06 24 MGP12 84005.10.0490 0.30 15 — — — 0.575 0.07 26 MGP1 84553.1 — — — — — — 0.519 0.2414 MGP1 84554.1 — — — — — — 0.542 0.12 19 MGP1 84554.2 0.0517 0.15 220.766 0.06 23 0.551 0.08 21 MGP1 84555.4 — — — — — — 0.516 0.27 13 CONT.— 0.0425 — — 0.624 — — 0.456 — — LYD887 84746.1 0.0589 L 41 1.05 L 53 —— — LYD868 86633.2 0.0521 0.02 25 0.963 0.02 40 — — — LYD868 86673.1 — —— 0.849 0.12 23 — — — LYD866 87309.5 — — — 0.780 0.30 13 — — — LYD86185566.3 0.0457 0.23 10 — — — — — — LYD861 85568.1 0.0478 0.14 15 — — — —— — LYD818 87321.2 — — — 0.803 0.21 17 0.602 0.08 19 LYD818 87321.40.0494 0.16 18 — — — — — — LYD818 87323.2 — — — 1.09 L 58 — — — LYD81786926.3 0.0684 L 64 1.05 L 53 — — — LYD817 86927.1 0.0529 L 27 0.9140.02 33 0.580 0.13 15 LYD773 87162.2 0.0487 0.13 17 0.839 0.08 22 — — —LYD773 87165.4 0.0622 L 49 1.13 L 64 — — — LYD768 87156.1 0.0510 0.01 220.830 0.10 20 — — — LYD721 87318.2 — — — 0.860 0.05 25 — — — LYD72187318.3 — — — 0.805 0.14 17 0.557 0.29 10 LYD721 87318.4 0.0509 0.04 220.958 0.01 39 — — — CONT. — 0.0417 — — 0.689 — — 0.505 — — MGP9 87204.20.0577 L 51 — — — — — — MGP9 87205.2 0.0449 0.28 18 — — — — — — MGP987205.3 0.0468 0.20 23 — — — — — — CONT. — 0.0381 — — — — — — — — LGP8585845.1 0.0389 L 38 0.841 L 48 — — — LGP85 85846.1 0.0389 L 38 0.6900.07 22 — — — LGP85 85846.3 0.0401 L 42 0.865 L 53 0.661 0.14 16 LGP8585846.5 0.0420 L 49 0.937 L 65 — — — LGP85 85849.1 0.0366 L 30 0.895 L58 — — — LGP105 85298.2 0.0455 L 62 0.921 L 62 — — — LGP105 85298.30.0366 L 30 0.935 L 65 — — — LGP105 85298.4 0.0441 L 57 1.03 L 81 0.712L 25 LGP105 85298.5 0.0413 L 47 0.893 L 58 — — — LGP105 85298.7 0.0409 L46 0.691 0.06 22 — — — LGP102 85930.3 0.0330 0.03 17 0.642 0.25 13 — — —LGP102 85931.2 0.0361 L 28 — — — — — — LGP102 85933.2 0.0417 L 48 0.7450.01 31 — — — LGP102 85933.3 0.0308 0.26 9 — — — — — — CONT. — 0.0281 —— 0.567 — — 0.571 — — LGP99 85617.3 0.0641 0.04 32 0.928 0.25 14 0.6390.09 15 LGP98 83620.7 0.0623 0.04 28 — — — — — — LGP97 83609.1 0.05610.23 15 — — — — — — LGP95 83695.1 — — — — — — 0.604 0.29 9 LGP95 83695.2— — — — — — 0.632 0.14 14 LGP87 85864.1 0.0673 L 38 — — — — — — LGP8684346.3 0.0627 0.05 29 — — — — — — LGP83 85755.1 0.0673 0.04 38 0.9840.18 21 — — — LGP83 85759.2 0.0565 0.23 16 0.963 0.07 18 — — — LGP8385759.4 0.0580 0.15 19 — — — 0.674 L 22 LGP110 85611.1 — — — — — — 0.6360.08 15 LGP110 85612.1 0.0634 0.06 30 — — — — — — LGP107 84338.1 0.05980.07 23 0.970 0.08 19 0.625 0.11 13 LGP106 85865.2 0.0570 0.26 17 — — —— — — LGP106 85869.2 0.0578 0.15 19 1.04 0.01 27 0.609 0.19 10 LGP10083691.2 — — — — — — 0.648 0.05 17 LGP100 83691.8 — — — — — — 0.595 0.237 CONT. — 0.0487 — — 0.815 — — 0.555 — — MGP9 85224.1 0.0433 0.22 17 — —— — — — MGP7 86137.1 0.0440 0.19 19 — — — — — — MGP7 86141.3 — — — 0.8270.17 26 0.655 0.09 17 CONT. — 0.0370 — — 0.659 — — 0.558 — — LYD91885320.2 — — — 0.924 0.03 37 0.576 0.02 23 LYD910 85212.1 — — — 0.8160.13 21 0.531 0.21 13 LYD880 85204.3 — — — — — — 0.534 0.11 14 LYD87285570.1 — — — — — — 0.570 0.06 22 LYD858 85796.1 — — — 0.828 0.07 230.521 0.23 11 LYD858 85797.1 0.0545 0.24 20 — — — — — — LYD857 86635.1 —— — 0.912 0.01 35 0.534 0.13 14 LYD857 86674.1 0.0540 0.18 19 1.03 L 530.579 0.04 24 LYD856 85693.2 0.0884 L 95 1.24 L 84 0.526 0.28 12 LYD85584609.3 0.0755 L 67 1.05 L 56 — — — LYD855 84609.4 0.0539 0.22 19 — — —— — — LYD852 85819.3 — — — 0.790 0.21 17 0.522 0.26 12 LYD815 84416.1 —— — 0.783 0.23 16 0.569 0.04 22 LYD815 84416.2 0.0575 0.12 27 — — — — —— LYD815 84416.3 — — — — — — 0.527 0.17 13 LYD810 84436.2 0.0683 L 511.00 L 49 — — — LYD810 84437.5 0.0532 0.25 17 0.975 L 44 0.607 L 30LYD807 84078.1 0.0514 0.28 13 — — — — — — LYD807 84080.1 0.0586 0.05 291.00 L 48 0.553 0.05 18 LYD802 85132.1 0.0667 0.02 47 1.05 0.07 56 0.5750.07 23 LYD801 84618.4 — — — 1.02 L 51 0.583 0.06 25 LYD792 85550.1 — —— 0.794 0.24 18 0.555 0.07 19 LYD792 85553.1 0.0612 0.01 35 0.931 L 380.565 0.02 21 LYD785 84430.1 — — — 0.850 0.11 26 0.534 0.24 14 LYD78584430.7 — — — 0.881 0.03 30 0.615 L 31 LYD782 85902.1 — — — 0.843 0.1125 — — — LYD782 85903.1 — — — 0.935 0.01 38 — — — LYD782 85904.3 — — —0.781 0.23 16 — — — LYD771 85463.1 — — — — — — 0.573 0.03 23 LYD77185463.3 — — — 0.865 0.05 28 — — — LYD771 85463.4 0.0580 0.09 28 0.8880.05 31 0.559 0.07 19 LYD723 84940.4 — — — 0.955 0.01 41 0.607 0.01 30LYD707 85707.1 — — — 0.867 0.03 28 0.528 0.14 13 LYD694 84125.1 0.0644 L42 1.07 L 58 0.527 0.11 13 CONT. — 0.0453 — — 0.675 — — 0.468 — — LYD90784978.1 0.0491 L 50 — — — — — — LYD906 84750.1 0.0433 L 32 0.643 0.15 19— — — LYD906 84754.1 0.0401 0.16 23 — — — — — — LYD904 84498.4 0.0449 L37 — — — — — — LYD904 84499.2 0.0439 0.02 34 0.696 0.02 29 0.629 0.02 20LYD903 85544.3 0.0429 L 31 0.646 0.13 20 — — — LYD903 85544.5 — — —0.604 0.30 12 — — — LYD902 84948.3 0.0387 0.11 18 — — — — — — LYD89087189.1 0.0372 0.24 14 — — — — — — LYD878 84487.3 0.0403 0.05 23 0.6250.16 16 — — — LYD878 84488.8 0.0482 0.01 48 0.681 0.06 26 — — — LYD86785535.1 0.0439 0.03 34 — — — — — — LYD858 85796.1 0.0420 0.02 29 — — — —— — LYD858 85797.1 0.0467 L 43 0.634 0.15 17 — — — LYD856 85693.2 0.04100.02 26 — — — — — — LYD825 85883.3 0.0375 0.21 15 — — — — — — LYD81285560.2 0.0430 0.04 32 0.629 0.18 16 0.600 0.12 14 LYD812 85563.4 0.04190.01 28 — — — — — — LYD812 85564.1 0.0381 0.15 17 — — — — — — LYD80787413.1 0.0392 0.18 20 — — — — — — LYD802 85132.1 0.0409 0.04 25 — — — —— — LYD792 85553.1 0.0449 0.03 37 — — — — — — LYD719 87356.3 — — — 0.6470.12 20 0.601 0.14 14 LYD718 85458.3 0.0442 0.03 35 — — — — — — LYD69985973.1 0.0386 0.09 18 — — — — — — CONT. — 0.0327 — — 0.541 — — 0.526 —— LGP82 83662.2 0.0413 L 19 0.783 L 41 — — — LGP82 83664.1 — — — — — —0.660 0.02 19 LGP82 83666.2 — — — 0.708 0.01 27 0.648 0.05 17 LGP8184957.3 0.0433 L 25 0.882 L 59 0.707 L 28 LGP81 84957.8 0.0371 0.25 70.651 0.09 17 0.620 0.20 12 LGP81 84958.2 — — — — — — 0.622 0.23 12LGP79 82510.1 — — — 0.680 0.03 22 0.627 0.18 13 LGP79 82510.2 — — —0.799 L 44 0.672 0.02 22 LGP79 82512.1 — — — 0.730 0.02 31 — — — LGP7982513.4 — — — 0.698 0.01 26 0.616 0.22 11 LGP78 82506.1 — — — 0.624 0.2612 0.629 0.16 14 LGP78 82507.1 — — — 0.627 0.18 13 0.635 0.11 15 LGP7882507.4 0.0398 0.18 15 0.793 L 43 — — — LGP78 82508.1 0.0377 0.17 90.669 0.04 20 0.618 0.19 12 LGP77 81452.2 — — — 0.659 0.06 19 — — —LGP77 81453.2 0.0441 L 27 0.738 L 33 — — — LGP77 81453.3 — — — 0.7110.01 28 0.643 0.08 16 LGP77 81454.1 0.0414 0.04 19 0.775 L 39 0.693 0.0125 LGP76 83653.1 — — — 0.620 0.26 12 — — — LGP76 83653.2 0.0402 0.05 160.738 0.02 33 — — — LGP76 83653.3 0.0408 0.17 18 0.805 L 45 — — — LGP7683654.1 0.0391 0.25 13 0.775 0.01 39 — — — LGP75 85309.1 — — — — — —0.691 L 25 LGP75 85309.4 0.0524 L 51 1.02 L 83 0.686 L 24 LGP75 87225.2— — — 0.622 0.29 12 — — — LGP74 81324.2 — — — 0.675 0.07 21 — — — LGP7481325.1 0.0429 L 24 0.952 L 71 0.627 0.18 13 LGP74 81326.4 — — — — — —0.612 0.22 11 LGP74 81328.1 — — — 0.654 0.07 18 0.620 0.15 12 LGP7381449.1 0.0473 L 36 0.987 L 77 0.745 L 35 LGP71 82500.4 0.0388 0.17 120.830 L 49 0.680 0.01 23 LGP71 82502.2 — — — 0.648 0.23 16 0.644 0.11 17LGP71 82502.3 0.0437 L 26 0.747 L 34 0.651 0.05 18 LGP71 82502.4 — — —0.653 0.09 17 — — — CONT. — 0.0347 — — 0.556 — — 0.553 — — LGP94 84352.60.0546 0.41 12 — — — — — — LGP90 85764.1 — — — — — — 0.605 0.37 9 CONT.— 0.0487 — — — — — 0.555 — — LYD758 85109.6 0.0528 0.40 17 — — — — — —CONT. — 0.0453 — — — — — — — — Table 183. “CONT.”—Control;“Ave.”—Average; “% Incr.” = % increment; “p-val.”—p-value, L- p < 0.01.

Results from T1 Plants

Tables 184-186 summarize the observed phenotypes of transgenic plantsexpressing the gene constructs using the TC-T1 Assays (seedling analysisof T1 plants).

The genes presented in Tables 184-186 showed a significant improvementin plant biomass and root development since they produced a higherbiomass (dry weight, Table 184), a larger leaf and root biomass (leafarea, root length and root coverage) (Table 185), and a higher relativegrowth rate of leaf area, and root coverage (Table 186) when grown undernormal growth conditions, compared to control plants grown underidentical growth conditions. Plants producing larger root biomass havebetter possibilities to absorb larger amount of nitrogen from soil.Plants producing larger leaf biomass have better ability to produceassimilates. The genes were cloned under the regulation of aconstitutive promoter (At6669; SEQ ID NO: 15751). The evaluation of eachgene was performed by testing the performance of different number ofevents. Some of the genes were evaluated in more than one tissue cultureassay. This second experiment confirmed the significant increment inleaf and root performance. Event with p-value<0.1 was consideredstatistically significant.

TABLE 184 Genes showing improved plant performance at Normal growthconditions under regulation of At6669 promoter Dry Weight [mg] Gene NameAve. P-Val. % Incr. LYD823 7.00 0.16 11 CONT. 6.30 — — LGP109 8.85 0.0121 LGP103 8.92 0.08 22 CONT. 7.31 — — LYD819 5.87 0.14 24 CONT. 4.71 — —Table 184. “CONT.”—Control; “Ave.”—Average; “% Incr.” = % increment;“p-val.”—p-value, L- p < 0.01.

TABLE 185 Genes showing improved plant performance at Normal growthconditions under regulation of At6669 promoter Roots Leaf Area [cm²]Coverage [cm²] Roots Length [cm] Gene P- % P- % P- % Name Ave. Val.Incr. Ave. Val. Incr. Ave. Val. Incr. LYD823 — — — 6.52 0.23 21 — — —CONT. — — — 5.37 — — — — — LGP109 0.632 0.12 11 — — — — — — LGP103 0.6310.20 11 — — — — — — CONT. 0.569 — — — — — — — — LYD763 0.496 0.14 175.01 0.15 32 5.49 0.18 14 CONT. 0.425 — — 3.80 — — 4.84 — — Table 185.“CONT.”—Control; “Ave.”—Average; “% Incr.” = % increment;“p-val.”—p-value, L- p < 0.01.

TABLE 186 Genes showing improved plant performance at Normal growthconditions under regulation of At6669 promoter RGR Of Leaf Area RGR OfRoots Coverage Gene Name Ave. P-Val. % Incr. Ave. P-Val. % Incr. LYD823— — — 0.770 0.24 23 CONT. — — — 0.629 — — LGP109 0.0610 0.28 10 — — —LGP103 0.0621 0.25 12 — — — CONT. 0.0553 — — — — — Table 186.“CONT.”—Control; “Ave.”—Average; “% Incr.” = % increment; “p-val.”—p-value, L- p < 0.01.

These results demonstrate that the polynucleotides of the invention arecapable of improving yield and additional valuable importantagricultural traits such as increase of biomass, abiotic stresstolerance, nitrogen use efficiency, yield, vigor, fiber yield and/orquality. Thus, transformed plants showing improved fresh and dry weightdemonstrate the gene capacity to improve biomass, a key trait of cropsfor forage and plant productivity; transformed plants showingimprovement of seed yield demonstrate the genes capacity to improveplant productivity; transformed plants showing improvement of plotcoverage and rosette diameter demonstrate the genes capacity to improveplant drought resistance as they reduce the loss of soil water by simpleevaporation and reduce the competition with weeds; hence reduce the needto use herbicides to control weeds. Transformed plants showingimprovement of relative growth rate of various organs (leaf and root)demonstrate the gene capacity to promote plant growth and henceshortening the needed growth period and/or alternatively improving theutilization of available nutrients and water leading to increase of landproductivity; Transformed plants showing improvement of organ number, asdemonstrated by the leaf number parameter, exhibit a potential toimprove biomass and yield important for forage and plant productivity;Transformed plants showing increased root length and coveragedemonstrate the gene capacity to improve drought resistance and betterutilization of fertilizers as the roots can reach larger soil volume;Transformed plants showing improvement of leaf petiole relative area andleaf blade area demonstrate the genes capacity to cope with limitedlight intensities results from increasing the plant population densitiesand hence improve land productivity.

Although the invention has been described in conjunction with specificembodiments thereof, it is evident that many alternatives, modificationsand variations will be apparent to those skilled in the art.Accordingly, it is intended to embrace all such alternatives,modifications and variations that fall within the spirit and broad scopeof the appended claims.

All publications, patents and patent applications mentioned in thisspecification are herein incorporated in their entirety by referenceinto the specification, to the same extent as if each individualpublication, patent or patent application was specifically andindividually indicated to be incorporated herein by reference. Inaddition, citation or identification of any reference in thisapplication shall not be construed as an admission that such referenceis available as prior art to the present invention. To the extent thatsection headings are used, they should not be construed as necessarilylimiting.

LENGTHY TABLES The patent application contains a lengthy table section.A copy of the table is available in electronic form from the USPTO website(http://seqdata.uspto.gov/?pageRequest=docDetail&DocID=US20160272987A1).An electronic copy of the table will also be available from the USPTOupon request and payment of the fee set forth in 37 CFR 1.19(b)(3).

1. A method of increasing yield, growth rate, biomass, vigor, oilcontent, seed yield, fiber yield, fiber quality, fiber length,photosynthetic capacity, nitrogen use efficiency, and/or abiotic stresstolerance of a plant, comprising expressing within the plant anexogenous polynucleotide comprising a nucleic acid sequence encoding apolypeptide at least 80% identical to SEQ ID NO: 885, 713-716, 718-734,737-741, 743-744, 746-765, 767-784, 786-788, 790-795, 797, 810-811,813-876, 878-884, 886-889, 891-929, 931-1021, 1029-1064, 1067-1074,1076-1080, 1082-1088, 1091-1092, 1094-1153, 9283-9526, 9536, 9550-9772,9825, 9832, 9843-9881, 9899, 9908, 9925-9988, 9990-10284, 10290-11275,11278-11279, 11282-11284, 11289-11295, 11297-11299, 11301, 11303-11305,11308-11312, 11314, 11384, 11386, 11394, 11400, 11407, 11416-11417,11421, 11425-11426, 11429, 11433, 11439-11441, 11443-11444, 11446-11447,11449-11450, 11453-11455, 11457, 11460, 11468-11469, 11471, 11475,11482, 11485, 11488, 11494-11496, 11500-11503, 11505-11506, 11510-11513,11516-11525, 11530, 11551, 11555, 11559, 11561, 11570-11571, 11582,11589, 11605, 11612, 11695, 11697, 11699-13027, 13057, 13066,13091-13092, 13104, 13109, 13116, 13119-13180, 13188, 13192-13327,13329-13352, 13355-13929, 13941-13942, 13946-14913, 14989-15034,15037-15049, 15051-15072, 15074-15221, 15229-15252, 15254-15272,15281-15409, 15425, 15428-15434, 15455-15721 or 15722, therebyincreasing the yield, growth rate, biomass, vigor, oil content, seedyield, fiber yield, fiber quality, fiber length, photosyntheticcapacity, nitrogen use efficiency, and/or abiotic stress tolerance ofthe plant.
 2. The method of claim 1, wherein said polypeptide is atleast 95% identical to the amino acid sequence selected from the groupconsisting of SEQ ID NOs: 885, 713-735, 737-741, 743-765, 767-795, 797,809-884, 886-1021, 1029-1064, 1067-1080, 1082-1092, 1094-1153,9276-9281, 9283-9532, 9534-9541, 9543-9545, 9548-9774, 9776, 9778-9785,9788-9791, 9793-9801, 9803, 9806-9807, 9809-9820, 9822-9823, 9825-9838,9840-9841, 9843-9881, 9889-9890, 9893-9894, 9897-9899, 9901, 9904, 9906,9908-9910, 9912-10285, 10287-11276, 11278-11319, 11321, 11323,11328-11330, 11333-11336, 11339-11342, 11344-11355, 11357, 11359-11362,11364-11366, 11369-13113, 13115-13944, 13946-14913, 14915, 14917-14918,14920-14921, 14923-14924, 14927-14933, 14937, 14939-14940, 14942,14944-14949, 14951, 14953, 14955-14958, 14960-14962, 14964-14971, 14973,14976, 14978-14979, 14989-15221, 15225-15272, 15275-15410, 15412-15420,15422-15423, 15425-15426, 15428-15434, 15436, 15440-15441, 15443-15444,15446, 15448-15449.
 3. A method of producing a crop comprising growing acrop plant transformed with an exogenous polynucleotide comprising anucleic acid sequence encoding a polypeptide at least 80% identical tothe amino acid sequence selected from the group consisting of SEQ IDNOs: 885, 713-716, 718-734, 737-741, 743-744, 746-765, 767-784, 786-788,790-795, 797, 810-811, 813-876, 878-884, 886-889, 891-929, 931-1021,1029-1064, 1067-1074, 1076-1080, 1082-1088, 1091-1092, 1094-1153,9283-9526, 9536, 9550-9772, 9825, 9832, 9843-9881, 9899, 9908,9925-9988, 9990-10284, 10290-11275, 11278-11279, 11282-11284,11289-11295, 11297-11299, 11301, 11303-11305, 11308-11312, 11314, 11384,11386, 11394, 11400, 11407, 11416-11417, 11421, 11425-11426, 11429,11433, 11439-11441, 11443-11444, 11446-11447, 11449-11450, 11453-11455,11457, 11460, 11468-11469, 11471, 11475, 11482, 11485, 11488,11494-11496, 11500-11503, 11505-11506, 11510-11513, 11516-11525, 11530,11551, 11555, 11559, 11561, 11570-11571, 11582, 11589, 11605, 11612,11695, 11697, 11699-13027, 13057, 13066, 13091-13092, 13104, 13109,13116, 13119-13180, 13188, 13192-13327, 13329-13352, 13355-13929,13941-13942, 13946-14913, 14989-15034, 15037-15049, 15051-15072,15074-15221, 15229-15252, 15254-15272, 15281-15409, 15425, 15428-15434,and 15455-15722, wherein the crop plant is derived from plants whichhave been transformed with said exogenous polynucleotide and which havebeen selected for increased yield, increased growth rate, increasedbiomass, increased vigor, increased oil content, increased seed yield,increased fiber yield, increased fiber quality, increased fiber length,increased photosynthetic capacity, increased nitrogen use efficiency,and/or increased abiotic stress tolerance as compared to a wild typeplant of the same species which is grown under the same growthconditions, and the crop plant having the increased yield, increasedgrowth rate, increased biomass, increased vigor, increased oil content,increased seed yield, increased fiber yield, increased fiber quality,increased fiber length, increased photosynthetic capacity, increasednitrogen use efficiency, and/or increased abiotic stress tolerance,thereby producing the crop.
 4. (canceled)
 5. The method of claim 1,wherein said exogenous polynucleotide comprises the nucleic acidsequence selected from the group consisting of SEQ ID NOs: 564, 4-86,88, 100-312, 320-389, 391, 395-475, 477, 489-563, 565-696, 704-709,1157-4245, 4247-8375, 8387-8683, and 8686-9275.
 6. (canceled)
 7. Anucleic acid construct comprising an isolated polynucleotide comprisinga nucleic acid sequence encoding a polypeptide which comprises an aminoacid sequence at least 80% identical to the amino acid sequence setforth in SEQ ID NO: 885, 713-716, 718-734, 737-741, 743-744, 746-765,767-784, 786-788, 790-795, 797, 810-811, 813-876, 878-884, 886-889,891-929, 931-1021, 1029-1064, 1067-1074, 1076-1080, 1082-1088,1091-1092, 1094-1153, 9283-9526, 9536, 9550-9772, 9825, 9832, 9843-9881,9899, 9908, 9925-9988, 9990-10284, 10290-11275, 11278-11279,11282-11284, 11289-11295, 11297-11299, 11301, 11303-11305, 11308-11312,11314, 11384, 11386, 11394, 11400, 11407, 11416-11417, 11421,11425-11426, 11429, 11433, 11439-11441, 11443-11444, 11446-11447,11449-11450, 11453-11455, 11457, 11460, 11468-11469, 11471, 11475,11482, 11485, 11488, 11494-11496, 11500-11503, 11505-11506, 11510-11513,11516-11525, 11530, 11551, 11555, 11559, 11561, 11570-11571, 11582,11589, 11605, 11612, 11695, 11697, 11699-13027, 13057, 13066,13091-13092, 13104, 13109, 13116, 13119-13180, 13188, 13192-13327,13329-13352, 13355-13929, 13941-13942, 13946-14913, 14989-15034,15037-15049, 15051-15072, 15074-15221, 15229-15252, 15254-15272,15281-15409, 15425, 15428-15434, 15455-15721 or 15722, and a promoterfor directing, transcription of said nucleic acid sequence in a hostcell, wherein said promoter is heterologous to said isolatedpolynucleotide and/or to said host cell, wherein said amino acidsequence is capable of increasing yield, growth rate, biomass, vigor,oil content, seed yield, fiber yield, fiber quality, fiber length,photosynthetic capacity, nitrogen use efficiency, and/or abiotic stresstolerance of a plant.
 8. The nucleic acid construct of claim 7, whereinsaid polypeptide is at least 95% identical to the amino acid sequenceselected from the group consisting of SEQ ID NOs: 885, 713-735, 737-741,743-765, 767-795, 797, 809-884, 886-1021, 1029-1064, 1067-1080,1082-1092, 1094-1153, 9276-9281, 9283-9532, 9534-9541, 9543-9545,9548-9774, 9776, 9778-9785, 9788-9791, 9793-9801, 9803, 9806-9807,9809-9820, 9822-9823, 9825-9838, 9840-9841, 9843-9881, 9889-9890,9893-9894, 9897-9899, 9901, 9904, 9906, 9908-9910, 9912-10285,10287-11276, 11278-11319, 11321, 11323, 11328-11330, 11333-11336,11339-11342, 11344-11355, 11357, 11359-11362, 11364-11366, 11369-13113,13115-13944, 13946-14913, 14915, 14917-14918, 14920-14921, 14923-14924,14927-14933, 14937, 14939-14940, 14942, 14944-14949, 14951, 14953,14955-14958, 14960-14962, 14964-14971, 14973, 14976, 14978-14979,14989-15221, 15225-15272, 15275-15410, 15412-15420, 15422-15423,15425-15426, 15428-15434, 15436, 15440-15441, 15443-15444, 15446,15448-15449, and 15451-15726.
 9. (canceled)
 10. The nucleic acidconstruct of claim 7, wherein said nucleic acid sequence is selectedfrom the group consisting of SEQ ID NOs: 564, 4-86, 88, 100-312,320-389, 391, 395-475, 477, 489-563, 565-696, 704-709, 1157-4245,4247-8375, 8387-8683, and 8686-9275.
 11. (canceled)
 12. The method ofclaim 1, wherein said polypeptide is selected from die group consistingof SEQ ID NOs: 885, 713-716, 718-734, 737-741, 743-744, 746-765,767-784, 786-788, 790-795, 797, 810-811, 813-876, 878-884, 886-889,891-929, 931-1021, 1029-1064, 1067-1074, 1076-1080, 1082-1088,1091-1092, 1094-1153, 9283-9526, 9536, 9550-9772, 9825, 9832, 9843-9881,9899, 9908, 9925-9988, 9990-10284, 10290-11275, 11278-11279,11282-11284, 11289-11295, 11297-11299, 11301, 11303-11305, 11308-11312,11314, 11384, 11386, 11394, 11400, 11407, 11416-11417, 11421,11425-11426, 11429, 11433, 11439-11441, 11443-11444, 11446-11447,11449-11450, 11453-11455, 11457, 11460, 11468-11469, 11471, 11475,11482, 11485, 11488, 11494-11496, 11500-11503, 11505-11506, 11510-11513,11516-11525, 11530, 11551, 11555, 11559, 11561, 11570-11571, 11582,11589, 11605, 11612, 11695, 11697, 11699-13027, 13057, 13066,13091-13092, 13104, 13109, 13116, 13119-13180, 13188, 13192-13327,13329-13352, 13355-13929, 13941-13942, 13946-14913, 14989-15034,15037-15049, 15051-15072, 15074-15221, 15229-15252, 15254-15272,15281-15409, 15425, 15428-15434, 15455-15721 and
 15722. 13. (canceled)14. A plant cell transformed with the nucleic acid construct of claim 7.15. (canceled)
 16. The method of claim 3, wherein said nucleic acidsequence encodes an amino acid sequence at least 95% identical to theamino acid sequence selected from the group consisting of SEQ ID NOs:885, 713-735, 737-741, 743-765, 767-795, 797, 809-884, 886-1021,1029-1064, 1067-1080, 1082-1092, 1094-1153, 9276-9281, 9283-9532,9534-9541, 9543-9545, 9548-9774, 9776, 9778-9785, 9788-9791, 9793-9801,9803, 9806-9807, 9809-9820, 9822-9823, 9825-9838, 9840-9841, 9843-9881,9889-9890, 9893-9894, 9897-9899, 9901, 9904, 9906, 9908-9910,9912-10285, 10287-11276, 11278-11319, 11321, 11323, 11328-11330,11333-11336, 11339-11342, 11344-11355, 11357, 11359-11362, 11364-11366,11369-13113, 13115-13944, 13946-14913, 14915, 14917-14918, 14920-14921,14923-14924, 14927-14933, 14937, 14939-14940, 14942, 14944-14949, 14951,14953, 14955-14958, 14960-14962, 14964-14971, 14973, 14976, 14978-14979,14989-15221, 15225-15272, 15275-15410, 15412-15420, 15422-15423,15425-15426, 15428-15434, 15436, 15440-15441, 15443-15444, 15446,15448-15449, and 15451-15726.
 17. The method of claim 3, wherein saidnucleic acid sequence is selected from the group consisting of SEQ IDNOs: 564, 4-86, 88, 100-312, 320-389, 391, 395-475, 477, 489-563,565-696, 704-709, 1157-4245, 4247-8375, 8387-8683, and 8686-9275. 18.(canceled)
 19. The method of claim 3, wherein said nucleic acid sequenceencodes the amino acid sequence selected from the group consisting ofSEQ ID NOs: 885, 713-735, 737-741, 743-765, 767-795, 797, 809-884,886-1021, 1029-1064, 1067-1080, 1082-1092, 1094-1153, 9276-9281,9283-9532, 9534-9541, 9543-9545, 9548-9774, 9776, 9778-9785, 9788-9791,9793-9801, 9803, 9806-9807, 9809-9820, 9822-9823, 9825-9838, 9840-9841,9843-9881, 9889-9890, 9893-9894, 9897-9899, 9901, 9904, 9906, 9908-9910,9912-10285, 10287-11276, 11278-11319, 11321, 11323, 11328-11330,11333-11336, 11339-11342, 11344-11355, 11357, 11359-11362, 11364-11366,11369-13113, 13115-13944, 13946-14913, 14915, 14917-14918, 14920-14921,14923-14924, 14927-14933, 14937, 14939-14940, 14942, 14944-14949, 14951,14953, 14955-14958, 14960-14962, 14964-14971, 14973, 14976, 14978-14979,14989-15221, 15225-15272, 15275-15410, 15412-15420, 15422-15423,15425-15426, 15428-15434, 15436, 15440-15441, 15443-15444, 15446,15448-15449, and 15451-15726.
 20. The plant cell of claim 14, whereinsaid plant cell forms part of a plant.
 21. The method of claim 1,further comprising growing the plant expressing said exogenouspolynucleotide under the abiotic stress.
 22. The method of any of claim1, wherein said abiotic stress is selected from the group consisting ofsalinity, drought, osmotic stress, water deprivation, flood, lowtemperature, high temperature, heavy metal toxicity, anaerobiosis,nutrient deficiency, nitrogen deficiency, nutrient excess, atmosphericpollution and UV irradiation.
 23. (canceled)
 24. A transgenic plantcomprising the nucleic acid construct of claim
 7. 25. The method ofclaim 1, further comprising growing the plant expressing said exogenouspolynucleotide under nitrogen-limiting conditions.
 26. (canceled)
 27. Amethod of growing a crop, the method comprising seeding seeds and/orplanting plantlets of a plant transformed with the nucleic acidconstruct of claim 7, wherein the plant is derived from plants whichhave been transformed with said exogenous polynucleotide and which havebeen selected for at least one trait selected from the group consistingof: increased nitrogen use efficiency, increased abiotic stresstolerance, increased biomass, increased growth rate, increased vigor,increased yield, increased fiber yield, increased fiber quality,increased fiber length, increased photosynthetic capacity, and increasedoil content as compared to a non-transformed plant, thereby growing thecrop. 28-30. (canceled)
 31. The method of claim 1, further comprisingselecting a plant having an increased yield, growth rate, biomass,vigor, oil content, seed yield, fiber yield, fiber quality, fiberlength, photosynthetic capacity, nitrogen use efficiency, and/or abioticstress tolerance as compared to the wild type plant of the same specieswhich is grown under the same growth conditions. 32-33. (canceled) 34.The method of claim 31, wherein said selecting is performed undernon-stress conditions.
 35. The method of claim 31, wherein saidselecting is performed under abiotic stress conditions.